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Platinum in PDB 2dqa: Crystal Structure of Tapes Japonica Lysozyme

Enzymatic activity of Crystal Structure of Tapes Japonica Lysozyme

All present enzymatic activity of Crystal Structure of Tapes Japonica Lysozyme:
3.2.1.17;

Protein crystallography data

The structure of Crystal Structure of Tapes Japonica Lysozyme, PDB code: 2dqa was solved by T.Goto, Y.Kakuta, Y.Abe, K.Takeshita, T.Imoto, T.Ueda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.86 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 42.749, 88.760, 43.644, 90.00, 116.04, 90.00
R / Rfree (%) 17.5 / 21

Platinum Binding Sites:

The binding sites of Platinum atom in the Crystal Structure of Tapes Japonica Lysozyme (pdb code 2dqa). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 8 binding sites of Platinum where determined in the Crystal Structure of Tapes Japonica Lysozyme, PDB code: 2dqa:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Platinum binding site 1 out of 8 in 2dqa

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Platinum binding site 1 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1201

b:33.9
occ:0.20
 PT A:PT1203 1.8 44.2 0.2
O A:HOH1477 2.0 59.6 1.0
O A:HOH1461 2.2 35.3 1.0
SD A:MET29 2.6 32.7 0.5
CE A:MET29 3.0 31.4 0.5
SD A:MET29 3.3 30.1 0.5
CG A:MET29 3.7 30.9 0.5
CG A:MET29 3.7 30.0 0.5
CB A:MET29 4.0 29.8 0.5
CB A:MET29 4.1 30.1 0.5
CD2 A:LEU34 4.1 23.3 1.0
CE A:MET29 4.2 30.2 0.5
CG A:LEU34 4.4 22.8 1.0

Platinum binding site 2 out of 8 in 2dqa

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Platinum binding site 2 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1202

b:24.4
occ:0.10
 O B:HOH2216 2.1 39.6 1.0
O A:HOH1454 2.1 37.6 1.0
O A:HOH1359 2.7 38.1 1.0
O B:HOH2198 2.8 51.4 1.0
CD A:LYS108 3.0 21.2 1.0
O6 B:NAG2004 3.4 22.1 1.0
CG A:LYS108 3.6 19.7 1.0
CE A:LYS108 4.1 22.1 1.0
NZ A:LYS108 4.3 22.5 1.0
C6 B:NAG2004 4.4 18.8 1.0
O B:HOH2175 4.7 27.5 1.0
N A:LYS108 4.8 17.6 1.0
CB A:LYS108 4.9 18.0 1.0
O B:HOH2126 5.0 62.9 1.0

Platinum binding site 3 out of 8 in 2dqa

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Platinum binding site 3 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1203

b:44.2
occ:0.20
 SD A:MET29 1.6 30.1 0.5
PT A:PT1201 1.8 33.9 0.2
CE A:MET29 2.0 31.4 0.5
SD A:MET29 2.0 32.7 0.5
O A:HOH1477 2.1 59.6 1.0
CG A:MET29 2.4 30.9 0.5
CG A:MET29 2.4 30.0 0.5
CE A:MET29 2.6 30.2 0.5
CB A:MET29 3.2 29.8 0.5
CB A:MET29 3.2 30.1 0.5
O A:HOH1461 3.4 35.3 1.0
CA A:MET29 4.5 29.9 0.5
CA A:MET29 4.5 29.8 0.5

Platinum binding site 4 out of 8 in 2dqa

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Platinum binding site 4 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1204

b:35.8
occ:0.10
 O A:HOH1444 2.0 42.2 1.0
O A:HOH1394 2.4 40.0 1.0
O A:HOH1406 2.5 39.2 1.0
O A:CYS101 4.0 19.7 1.0
CA A:HIS102 4.1 20.5 1.0
ND1 A:HIS102 4.2 21.9 1.0
O A:HOH1321 4.3 28.3 1.0
NH2 A:ARG92 4.3 16.6 1.0
C A:HIS102 4.5 21.1 1.0
O A:HIS102 4.5 21.4 1.0
NH1 A:ARG92 4.6 17.1 1.0
CB A:HIS102 4.7 20.4 1.0
CZ A:ARG92 5.0 15.6 1.0
C A:CYS101 5.0 19.2 1.0
CG A:HIS102 5.0 20.9 1.0

Platinum binding site 5 out of 8 in 2dqa

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Platinum binding site 5 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt1208

b:24.3
occ:0.10
 O A:HOH1441 2.1 18.7 1.0
O A:HOH1424 2.3 28.9 1.0
O A:HOH1430 2.9 45.6 1.0
O A:HOH1341 3.0 39.2 1.0
O6 A:NAG1205 3.1 17.4 0.5
C1 A:NAG1206 4.1 14.7 1.0
C6 A:NAG1205 4.1 16.6 0.5
N2 A:NAG1206 4.2 18.1 1.0
C6 A:NAG1205 4.3 16.1 0.5
O A:HOH1428 4.4 22.4 1.0
C4 A:NAG1205 4.5 15.0 0.5
C4 A:NAG1205 4.6 14.7 0.5
C2 A:NAG1206 4.6 16.1 1.0
O A:HOH1373 4.6 15.4 1.0
O4 A:NAG1205 4.7 15.4 0.5
C3 A:NAG1206 4.7 16.2 1.0
O4 A:NAG1205 4.8 15.3 0.5
CG A:PRO44 4.8 14.2 1.0
C5 A:NAG1205 4.8 15.8 0.5
O5 A:NAG1206 4.9 14.8 1.0
C5 A:NAG1206 4.9 14.3 1.0
C5 A:NAG1205 5.0 15.3 0.5

Platinum binding site 6 out of 8 in 2dqa

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Platinum binding site 6 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2003

b:35.1
occ:0.40
 O B:HOH2257 1.6 21.3 1.0
SD B:MET29 2.0 30.5 1.0
O B:HOH2271 2.3 61.9 1.0
CG B:MET29 3.1 28.5 1.0
CB B:MET29 3.4 27.4 1.0
CE B:MET29 3.5 28.7 1.0
CD1 B:LEU34 4.3 19.1 0.5
CG B:LEU34 4.4 19.6 0.5
CD2 B:LEU34 4.6 19.5 0.5
CA B:MET29 4.7 27.5 1.0

Platinum binding site 7 out of 8 in 2dqa

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Platinum binding site 7 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2007

b:18.9
occ:0.20
 O B:HOH2231 2.0 49.4 1.0
O B:HOH2223 2.0 27.8 1.0
PT B:PT2008 2.2 21.7 0.1
N2 B:NAG2005 3.5 18.1 1.0
C3 B:NAG2005 3.7 16.5 1.0
C2 B:NAG2005 4.1 16.5 1.0
O B:HOH2265 4.3 18.1 1.0
O3 B:NAG2005 4.3 17.6 1.0
C1 B:NAG2005 4.4 15.0 1.0
C7 B:NAG2005 4.5 19.7 1.0
O B:HOH2166 4.6 26.4 1.0
C8 B:NAG2005 4.7 20.4 1.0
C4 B:NAG2005 4.8 15.6 1.0
C5 B:NAG2005 5.0 14.8 1.0

Platinum binding site 8 out of 8 in 2dqa

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Platinum binding site 8 out of 8 in the Crystal Structure of Tapes Japonica Lysozyme


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 Tapes Japonica Lysozyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pt2008

b:21.7
occ:0.10
 O B:HOH2223 1.9 27.8 1.0
O B:HOH2265 2.1 18.1 1.0
PT B:PT2007 2.2 18.9 0.2
O B:HOH2204 3.6 38.7 1.0
O B:HOH2231 3.9 49.4 1.0
C1 B:NAG2005 4.0 15.0 1.0
N2 B:NAG2005 4.2 18.1 1.0
O B:HOH2101 4.3 21.8 1.0
C2 B:NAG2005 4.5 16.5 1.0
O B:HOH2200 4.5 15.6 1.0
C3 B:NAG2005 4.6 16.5 1.0
CG B:PRO44 4.6 13.1 1.0
C5 B:NAG2005 4.7 14.8 1.0
C4 B:NAG2004 4.7 16.1 1.0
C6 B:NAG2004 4.8 18.8 1.0
O5 B:NAG2005 4.8 15.6 1.0
O4 B:NAG2004 4.8 16.1 1.0
CB B:PRO44 5.0 12.8 1.0

Reference:

T.Goto, Y.Abe, Y.Kakuta, K.Takeshita, T.Imoto, T.Ueda. Crystal Structure of Tapes Japonica Lysozyme with Substrate Analogue: Structural Basis of the Catalytic Mechanism and Manifestation of Its Chitinase Activity Accompanied By Quaternary Structural Change J.Biol.Chem. V. 282 27459 2007.
ISSN: ISSN 0021-9258
PubMed: 17631496
DOI: 10.1074/JBC.M704555200
Page generated: Thu Oct 10 10:41:44 2024

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