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Platinum in PDB 3w3s: Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs

Enzymatic activity of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs

All present enzymatic activity of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs:
6.1.1.11;

Protein crystallography data

The structure of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs, PDB code: 3w3s was solved by Y.Itoh, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.82 / 3.10
Space group I 4 3 2
Cell size a, b, c (Å), α, β, γ (°) 272.817, 272.817, 272.817, 90.00, 90.00, 90.00
R / Rfree (%) 20.4 / 26

Other elements in 3w3s:

The structure of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Platinum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Platinum atom in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs (pdb code 3w3s). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 15 binding sites of Platinum where determined in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs, PDB code: 3w3s:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 15 in 3w3s

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Platinum binding site 1 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2003

b:91.0
occ:0.50
 N3 A:SSA2002 0.9 71.4 0.5
C4 A:SSA2002 1.1 65.9 0.5
N9 A:SSA2002 1.6 56.8 0.5
C1' A:SSA2002 2.1 65.2 0.5
C2 A:SSA2002 2.2 54.5 0.5
C5 A:SSA2002 2.5 55.5 0.5
C2' A:SSA2002 2.8 76.8 0.5
C8 A:SSA2002 2.9 58.6 0.5
N1 A:SSA2002 3.2 55.8 0.5
C6 A:SSA2002 3.3 63.1 0.5
N7 A:SSA2002 3.3 56.6 0.5
O4' A:SSA2002 3.4 73.3 0.5
O2' A:SSA2002 3.5 79.1 0.5
CG A:ARG485 3.7 0.2 1.0
CD1 A:PHE364 3.7 61.9 1.0
CG A:PHE364 3.8 65.4 1.0
CZ A:ARG485 3.9 0.8 1.0
NE A:ARG485 4.0 0.5 1.0
C3' A:SSA2002 4.0 82.2 0.5
CE1 A:PHE364 4.1 68.5 1.0
NH1 A:ARG485 4.1 0.4 1.0
NH2 A:ARG485 4.1 0.8 1.0
CB A:PHE364 4.2 71.6 1.0
CD2 A:PHE364 4.2 69.6 1.0
C4' A:SSA2002 4.4 81.3 0.5
CA A:GLY482 4.4 90.9 1.0
CD A:ARG485 4.5 0.1 1.0
CZ A:PHE364 4.5 70.0 1.0
CE2 A:PHE364 4.6 69.3 1.0
N6 A:SSA2002 4.6 70.2 0.5
CB A:ARG485 4.8 0.9 1.0

Platinum binding site 2 out of 15 in 3w3s

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Platinum binding site 2 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2004

b:0.8
occ:0.25
 CZ A:PHE409 0.9 0.2 0.8
CE2 A:PHE409 1.2 0.6 0.8
CE1 A:PHE409 1.2 0.3 0.8
CD1 A:PHE409 1.8 0.4 0.8
CD2 A:PHE409 1.8 0.2 0.8
CG A:PHE409 2.0 0.4 0.8
CD2 A:TYR410 2.8 85.3 0.8
CB A:PHE409 3.5 0.8 0.8
CE2 A:TYR410 3.5 90.5 0.8
N10 A:SSA2002 3.8 76.4 0.5
CG A:TYR410 3.8 92.9 0.8
N A:TYR410 3.9 0.3 0.8
CB A:TYR410 4.0 98.8 0.8
ND2 A:ASN454 4.1 94.6 1.0
CA A:PHE409 4.3 0.3 0.8
N A:PHE409 4.3 0.2 0.8
CA A:SSA2002 4.4 71.5 0.5
C A:PHE409 4.5 0.9 0.8
CA A:TYR410 4.6 0.1 0.8
ZN A:ZN2001 4.6 0.2 1.0
CD2 A:HIS456 4.6 0.1 1.0
NE2 A:HIS456 4.6 0.9 1.0
SG A:CYS478 4.8 0.4 1.0
CG A:ASN454 4.8 94.5 1.0
CZ A:TYR410 4.9 97.4 0.8
CZ A:PHE460 5.0 86.9 1.0

Platinum binding site 3 out of 15 in 3w3s

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Platinum binding site 3 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2005

b:0.6
occ:1.00
 CD A:ARG90 4.2 94.6 1.0
CG A:ARG87 4.5 0.1 1.0
CE A:LYS91 4.5 1.0 1.0
NE A:ARG90 4.9 95.3 1.0
CD A:ARG87 5.0 0.1 1.0

Platinum binding site 4 out of 15 in 3w3s

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Platinum binding site 4 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2006

b:0.2
occ:1.00
 O4' B:U47C 3.6 99.8 1.0
CB A:GLU75 3.9 75.6 1.0
CD A:GLU75 4.0 84.7 1.0
C1' B:U47C 4.0 0.2 1.0
C4' B:U47C 4.0 89.6 1.0
OE1 A:GLU75 4.0 85.7 1.0
CG A:GLU75 4.1 77.4 1.0
O2' B:U47C 4.3 92.1 1.0
OE2 A:GLU75 4.4 90.1 1.0
C2' B:U47C 4.7 95.1 1.0
C5' B:U47C 4.9 0.9 1.0
NH1 A:ARG72 4.9 0.4 1.0

Platinum binding site 5 out of 15 in 3w3s

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Platinum binding site 5 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2007

b:0.3
occ:0.50
 CE1 A:HIS74 2.6 0.1 1.0
NE2 A:HIS74 2.9 0.9 1.0
CD A:ARG72 3.7 0.9 1.0
ND1 A:HIS74 3.8 0.8 1.0
OD2 A:ASP153 3.9 0.7 1.0
OD1 A:ASP153 4.0 0.1 1.0
CD2 A:HIS74 4.2 0.6 1.0
CG A:ASP153 4.3 0.2 1.0
O A:LEU147 4.4 88.2 1.0
NE A:ARG72 4.5 0.1 1.0
CG A:HIS74 4.6 0.7 1.0
CD2 A:HIS150 4.7 0.1 1.0
CD2 A:LEU147 4.7 79.7 1.0
CB A:ARG72 4.9 94.7 1.0
CG A:ARG72 4.9 97.1 1.0

Platinum binding site 6 out of 15 in 3w3s

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Platinum binding site 6 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2008

b:0.5
occ:0.50
 CA A:ARG148 4.1 93.3 1.0
N A:ARG148 4.2 87.2 1.0
OE2 A:GLU144 4.3 0.8 1.0
CB A:ARG148 4.4 0.2 1.0
SE A:MSE78 4.4 0.8 1.0
CG A:GLU144 4.5 0.3 1.0
C A:LEU147 4.5 89.7 1.0
CB A:LEU147 4.7 88.9 1.0
CG A:ARG148 4.7 0.8 1.0
O A:GLU144 4.7 0.2 1.0
O A:LEU147 4.7 88.2 1.0
CD A:GLU144 4.9 0.3 1.0
CD2 A:HIS74 4.9 0.6 1.0

Platinum binding site 7 out of 15 in 3w3s

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Platinum binding site 7 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2009

b:0.8
occ:0.50
 NH2 A:ARG260 3.3 0.2 1.0
NE2 A:HIS263 3.3 0.7 1.0
CD2 A:HIS263 3.3 1.0 1.0
CD2 A:LEU416 3.3 0.5 0.8
CZ A:ARG260 3.9 0.3 1.0
CD A:ARG260 4.1 0.1 1.0
NE A:ARG260 4.2 0.7 1.0
CE1 A:HIS263 4.3 0.1 1.0
CG A:HIS263 4.3 1.0 1.0
NH1 A:ARG260 4.7 0.5 1.0
CG A:LEU416 4.8 0.4 0.8
ND1 A:HIS263 4.8 0.3 1.0

Platinum binding site 8 out of 15 in 3w3s

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Platinum binding site 8 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2010

b:0.6
occ:0.50
 OE1 A:GLU105 2.6 0.3 1.0
OE2 A:GLU105 2.8 0.7 1.0
CD A:GLU105 3.0 0.7 1.0
CD A:ARG136 4.0 0.4 1.0
CG A:GLU105 4.4 0.6 1.0
NE A:ARG136 4.6 0.7 1.0
NH2 A:ARG103 4.8 0.9 1.0
CG2 A:VAL107 4.9 72.5 1.0
NH2 A:ARG136 4.9 0.6 1.0

Platinum binding site 9 out of 15 in 3w3s

Go back to Platinum Binding Sites List in 3w3s
Platinum binding site 9 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2011

b:0.7
occ:0.50
 CB A:PRO375 3.9 0.3 1.0
OE2 A:GLU422 4.0 0.1 1.0
CG A:PRO375 4.3 98.0 1.0
CD A:PRO375 4.9 0.3 1.0

Platinum binding site 10 out of 15 in 3w3s

Go back to Platinum Binding Sites List in 3w3s
Platinum binding site 10 out of 15 in the Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of Crystal Structure of A. Aeolicus Trnasec in Complex with M. Kandleri Serrs within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt2012

b:0.1
occ:0.50
 CA A:GLY194 3.3 0.8 1.0
N A:GLY194 3.4 0.8 1.0
C A:ARG193 3.7 1.0 1.0
O A:ARG193 4.1 0.2 1.0
CA A:ARG193 4.4 0.5 1.0
CB A:ARG193 4.4 0.3 1.0
N A:ARG193 4.6 0.6 1.0
CE1 A:PHE192 4.7 0.6 1.0
C A:GLY194 4.8 0.5 1.0
CZ A:PHE192 4.9 0.4 1.0

Reference:

Y.Itoh, S.Sekine, S.Suetsugu, S.Yokoyama. Tertiary Structure of Bacterial Selenocysteine Trna Nucleic Acids Res. V. 41 6729 2013.
ISSN: ISSN 0305-1048
PubMed: 23649835
DOI: 10.1093/NAR/GKT321
Page generated: Thu Oct 10 10:52:10 2024

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