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Platinum in PDB 4qi7: Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh

Protein crystallography data

The structure of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh, PDB code: 4qi7 was solved by T.C.Tan, R.Gandini, C.Sygmund, R.Kittl, D.Haltrich, R.Ludwig, B.M.Hallberg, C.Divne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.04 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 133.599, 141.851, 146.998, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 23.5

Other elements in 4qi7:

The structure of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh also contains other interesting chemical elements:

Magnesium (Mg) 4 atoms
Iron (Fe) 2 atoms

Platinum Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Platinum atom in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh (pdb code 4qi7). This binding sites where shown within 5.0 Angstroms radius around Platinum atom.
In total 20 binding sites of Platinum where determined in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh, PDB code: 4qi7:
Jump to Platinum binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Platinum binding site 1 out of 20 in 4qi7

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Platinum binding site 1 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 1 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt912

b:84.3
occ:1.00
N A:PRO781 4.1 51.7 1.0
CA A:PRO781 4.1 41.9 1.0
CG A:PRO781 4.3 55.7 1.0
C A:GLY780 4.3 47.9 1.0
CD A:PRO781 4.4 51.7 1.0
CB A:PRO781 4.5 40.4 1.0
CA A:GLY780 4.7 38.3 1.0
NH1 A:ARG713 4.7 78.2 1.0
CD A:ARG713 4.7 40.6 1.0
O A:TRP518 4.8 45.8 1.0
O A:GLY780 4.8 70.7 1.0

Platinum binding site 2 out of 20 in 4qi7

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Platinum binding site 2 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 2 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt913

b:0.9
occ:0.96
CB B:LEU563 4.1 63.4 1.0
CB A:LYS427 4.2 29.3 1.0
CD1 B:LEU563 4.2 46.0 1.0
CE A:LYS427 4.3 54.0 1.0
CD A:LYS427 4.4 28.0 1.0
NZ A:LYS427 4.4 48.6 1.0
CG B:LEU563 4.5 56.7 1.0
O A:LYS427 4.6 61.2 1.0
CD2 B:LEU563 4.6 60.8 1.0
C A:LYS427 4.8 50.9 1.0
CG2 B:THR280 4.8 83.4 1.0
CG A:LYS427 4.8 27.0 1.0

Platinum binding site 3 out of 20 in 4qi7

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Platinum binding site 3 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 3 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt914

b:0.1
occ:0.83
N A:ASP647 3.9 48.4 1.0
CA A:ASP647 4.0 46.3 1.0
C A:LYS646 4.2 55.0 1.0
O A:LYS646 4.3 64.4 1.0
CB A:ASP647 4.5 62.0 1.0
CB A:LYS646 4.5 38.7 1.0
CD A:PRO648 4.8 51.2 1.0
CA A:LYS646 5.0 38.8 1.0

Platinum binding site 4 out of 20 in 4qi7

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Platinum binding site 4 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 4 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt915

b:0.5
occ:0.61
CB A:PRO468 4.2 38.5 1.0
CG2 A:ILE466 4.8 32.5 1.0
CG A:PRO468 4.9 37.2 1.0
OG1 A:THR451 4.9 47.7 1.0
CA A:PRO468 5.0 46.5 1.0

Platinum binding site 5 out of 20 in 4qi7

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Platinum binding site 5 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 5 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt916

b:0.6
occ:0.65
NZ A:LYS331 2.8 0.4 1.0
CD1 A:TYR335 3.9 51.5 1.0
CE A:LYS331 4.2 0.0 1.0
CE1 A:TYR335 4.3 62.2 1.0
CG A:TYR335 5.0 63.1 1.0

Platinum binding site 6 out of 20 in 4qi7

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Platinum binding site 6 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 6 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt917

b:0.6
occ:0.61
O A:LYS273 3.5 73.7 1.0
C A:LYS273 4.6 80.0 1.0
N A:LYS273 4.8 75.5 1.0
CZ2 A:TRP551 4.9 72.8 1.0

Platinum binding site 7 out of 20 in 4qi7

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Platinum binding site 7 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 7 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt918

b:0.4
occ:0.56
NE A:ARG697 3.9 41.1 1.0
CH2 A:TRP295 4.1 72.2 1.0
NH2 A:ARG697 4.2 61.5 1.0
CZ3 A:TRP295 4.3 67.2 1.0
CZ A:ARG697 4.4 57.5 1.0
ND2 A:ASN699 4.7 53.4 1.0
CZ2 A:TRP295 4.7 70.4 1.0
OD1 A:ASN699 4.7 74.1 1.0
CD A:ARG697 4.7 38.2 1.0
CG A:ARG697 4.8 35.8 1.0
O A:ARG697 4.9 56.1 1.0
CE3 A:TRP295 5.0 60.2 1.0
O A:GLN694 5.0 66.1 1.0

Platinum binding site 8 out of 20 in 4qi7

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Platinum binding site 8 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 8 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt919

b:0.8
occ:1.00
NZ A:LYS433 2.4 20.4 1.0
CE A:LYS433 3.3 95.2 1.0
CD A:LYS433 3.8 91.3 1.0
CG1 A:VAL228 4.3 58.7 1.0
CG2 A:VAL228 4.6 52.0 1.0
CG A:PRO225 4.7 72.2 1.0
CB A:PRO225 4.9 67.0 1.0

Platinum binding site 9 out of 20 in 4qi7

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Platinum binding site 9 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 9 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt920

b:0.3
occ:0.52
O A:ALA761 4.2 60.9 1.0
CB A:ALA761 4.3 25.2 1.0
C A:ALA761 4.3 52.4 1.0
N A:LYS762 4.5 50.4 1.0
CA A:LYS762 4.6 51.1 1.0
CB A:ALA765 4.7 51.1 1.0
CG A:LYS762 4.8 43.5 1.0

Platinum binding site 10 out of 20 in 4qi7

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Platinum binding site 10 out of 20 in the Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh


Mono view


Stereo pair view

A full contact list of Platinum with other atoms in the Pt binding site number 10 of Cellobiose Dehydrogenase From Neurospora Crassa, Nccdh within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pt921

b:0.4
occ:1.00
CA A:SER189 4.3 0.3 1.0
CB A:SER189 4.4 0.2 1.0
N A:SER189 4.6 0.1 1.0
OG A:SER189 4.7 0.4 1.0

Reference:

T.C.Tan, D.Kracher, R.Gandini, C.Sygmund, R.Kittl, D.Haltrich, B.M.Hallberg, R.Ludwig, C.Divne. Structural Basis For Cellobiose Dehydrogenase Action During Oxidative Cellulose Degradation. Nat Commun V. 6 7542 2015.
ISSN: ESSN 2041-1723
PubMed: 26151670
DOI: 10.1038/NCOMMS8542
Page generated: Wed Dec 16 02:05:02 2020

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