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Zinc in PDB 2d0w: Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans

Protein crystallography data

The structure of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans, PDB code: 2d0w was solved by M.Nojiri, D.Hira, K.Yamaguchi, S.Suzuki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.24 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.779, 57.283, 67.007, 90.00, 101.55, 90.00
R / Rfree (%) 18.5 / 19.1

Other elements in 2d0w:

The structure of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans also contains other interesting chemical elements:

Iron (Fe) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans (pdb code 2d0w). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans, PDB code: 2d0w:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 2d0w

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Zinc binding site 1 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1205

b:21.9
occ:1.00
 OE1 A:GLU68 1.8 15.2 1.0
ND1 A:HIS65 1.9 17.6 1.0
N A:HIS65 2.2 16.2 1.0
CD A:GLU68 2.7 15.5 1.0
CG A:HIS65 2.9 17.4 1.0
OE2 A:GLU68 2.9 15.0 1.0
CE1 A:HIS65 3.0 17.7 1.0
C A:GLY64 3.1 16.3 1.0
CA A:HIS65 3.1 17.1 1.0
CB A:HIS65 3.2 18.2 1.0
CA A:GLY64 3.3 15.2 1.0
N A:ILE66 3.7 17.7 1.0
C A:HIS65 3.9 18.1 1.0
CD2 A:HIS65 4.0 17.9 1.0
NE2 A:HIS65 4.0 16.6 1.0
O A:HOH1246 4.1 26.6 1.0
CG A:GLU68 4.2 17.4 1.0
O A:GLY64 4.3 18.0 1.0
CE A:LYS70 4.6 36.6 1.0
N A:GLY64 4.7 13.7 1.0
O A:HOH1357 4.8 35.5 1.0

Zinc binding site 2 out of 10 in 2d0w

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Zinc binding site 2 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1206

b:20.6
occ:1.00
 O A:HOH1424 2.2 5.7 1.0
OD1 A:ASP109 2.2 19.1 1.0
ND1 A:HIS106 2.2 17.4 1.0
CG A:HIS106 3.1 15.5 1.0
CG A:ASP109 3.1 18.2 1.0
CB A:HIS106 3.3 14.3 1.0
CE1 A:HIS106 3.3 17.5 1.0
CB A:ASP109 3.4 16.9 1.0
CA A:HIS106 3.9 14.2 1.0
O A:HOH1369 4.1 36.5 1.0
CD2 A:HIS106 4.3 16.8 1.0
OD2 A:ASP109 4.3 19.5 1.0
NE2 A:HIS106 4.3 19.2 1.0
O A:HIS106 4.6 15.7 1.0
CB A:SER58 4.6 16.8 1.0
OG A:SER58 4.6 15.8 1.0
CBB A:HEM200 4.6 9.5 1.0
C A:HIS106 4.8 14.8 1.0
O A:PRO105 4.9 14.6 1.0
CA A:ASP109 4.9 19.2 1.0
O A:HOH1254 5.0 42.0 1.0

Zinc binding site 3 out of 10 in 2d0w

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Zinc binding site 3 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1214

b:45.0
occ:1.00
 OD2 A:ASP77 2.3 27.5 1.0
O A:TYR79 2.3 18.5 1.0
O A:HOH1252 2.4 14.2 1.0
O A:GLY74 2.5 15.3 1.0
O A:HOH1225 2.6 23.9 1.0
O A:HOH1235 2.6 20.1 1.0
CG A:ASP77 3.4 26.3 1.0
C A:TYR79 3.5 18.7 1.0
C A:GLY74 3.6 15.4 1.0
OD1 A:ASP77 3.9 31.1 1.0
CA A:TYR79 4.3 20.2 1.0
CA A:LEU75 4.4 12.9 1.0
N A:LEU75 4.4 13.7 1.0
O A:ASP77 4.4 17.1 1.0
N A:TYR79 4.4 19.5 1.0
N A:TRP80 4.5 19.5 1.0
CA A:GLY74 4.5 15.5 1.0
O2A A:HEM200 4.5 17.3 1.0
N A:ASP77 4.5 16.6 1.0
CB A:TYR79 4.5 19.9 1.0
CA A:TRP80 4.6 18.2 1.0
CB A:ASP77 4.6 23.7 1.0
C A:ASP77 4.6 18.9 1.0
CD2 A:TYR79 4.7 23.2 1.0
N A:GLY74 4.7 13.7 1.0
C A:LEU75 4.8 14.6 1.0
CE3 A:TRP80 4.8 21.6 1.0
CA A:ASP77 4.8 19.3 1.0
CD2 A:TRP80 4.8 20.8 1.0
O A:HOH1365 4.8 36.9 1.0
N A:ASN76 5.0 13.2 1.0

Zinc binding site 4 out of 10 in 2d0w

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Zinc binding site 4 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1220

b:42.5
occ:1.00
 OE1 A:GLU153 2.2 29.9 1.0
O A:HOH1309 2.5 26.4 1.0
CD A:GLU153 3.0 26.5 1.0
OE2 A:GLU153 3.0 23.4 1.0
O A:HOH1300 3.9 30.6 1.0
OE2 A:GLU52 3.9 25.0 1.0
NZ A:LYS157 4.0 20.1 1.0
CD1 A:ILE149 4.4 20.0 1.0
CG A:GLU153 4.5 23.9 1.0
CD1 A:LEU56 4.7 18.9 1.0
CE A:LYS157 4.8 23.4 1.0
O A:HOH1260 4.9 22.6 1.0
CD A:GLU52 4.9 22.0 1.0

Zinc binding site 5 out of 10 in 2d0w

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Zinc binding site 5 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1222

b:69.4
occ:1.00
 O A:HOH1443 3.7 51.8 1.0
OE1 B:GLU111 3.9 26.0 1.0
OD1 A:ASP26 4.2 31.9 1.0
O A:HOH1387 4.2 56.0 1.0
OE2 B:GLU111 4.3 24.3 1.0
O B:HOH1325 4.4 39.9 1.0
O B:HOH1310 4.4 51.4 1.0
OD2 A:ASP26 4.5 31.2 1.0
OE1 B:GLU23 4.5 35.5 1.0
CD B:GLU111 4.6 23.4 1.0
CG A:ASP26 4.8 30.1 1.0
NZ A:LYS31 4.9 33.4 1.0

Zinc binding site 6 out of 10 in 2d0w

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Zinc binding site 6 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:38.7
occ:1.00
 O B:TYR79 2.1 22.8 1.0
O B:HOH1432 2.1 23.6 1.0
OD1 B:ASP77 2.3 24.1 1.0
O B:HOH1225 2.3 31.6 1.0
O B:HOH1313 2.4 17.5 1.0
OD2 B:ASP77 2.7 25.5 1.0
CG B:ASP77 2.8 25.3 1.0
O B:GLY74 2.8 21.1 1.0
C B:TYR79 3.3 22.9 1.0
C B:GLY74 3.8 19.9 1.0
N B:TYR79 4.1 24.4 1.0
CA B:TYR79 4.1 22.0 1.0
CB B:ASP77 4.2 23.4 1.0
O B:ASP77 4.2 23.8 1.0
N B:TRP80 4.3 22.0 1.0
O B:HOH1317 4.3 33.5 1.0
CB B:TYR79 4.5 21.5 1.0
C B:ASP77 4.5 22.8 1.0
CA B:TRP80 4.5 22.3 1.0
N B:ASP77 4.5 19.7 1.0
O2A B:HEM201 4.6 18.7 1.0
N B:LEU75 4.6 18.9 1.0
CA B:GLY74 4.6 19.1 1.0
CA B:LEU75 4.6 17.2 1.0
CA B:ASP77 4.7 22.1 1.0
CD2 B:TRP80 4.8 21.1 1.0
N B:GLY74 4.8 18.9 1.0
CD2 B:TYR79 4.8 21.3 1.0
CE3 B:TRP80 4.8 20.9 1.0
O B:HOH1387 4.8 40.5 1.0
C B:LEU75 4.9 17.7 1.0

Zinc binding site 7 out of 10 in 2d0w

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Zinc binding site 7 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1207

b:18.4
occ:1.00
 OE1 B:GLU68 1.8 19.3 1.0
N B:HIS65 2.0 17.2 1.0
ND1 B:HIS65 2.2 20.3 1.0
CD B:GLU68 2.7 18.9 1.0
C B:GLY64 2.9 17.3 1.0
CA B:GLY64 3.0 16.3 1.0
OE2 B:GLU68 3.1 16.9 1.0
CG B:HIS65 3.1 18.6 1.0
CA B:HIS65 3.1 18.0 1.0
CE1 B:HIS65 3.2 22.1 1.0
CB B:HIS65 3.3 18.9 1.0
N B:ILE66 3.7 19.4 1.0
C B:HIS65 4.0 18.4 1.0
O B:HOH1253 4.1 17.2 0.5
O B:GLY64 4.1 16.3 1.0
CG B:GLU68 4.1 18.5 1.0
CD2 B:HIS65 4.2 20.2 1.0
NE2 B:HIS65 4.3 21.9 1.0
N B:GLY64 4.5 14.4 1.0

Zinc binding site 8 out of 10 in 2d0w

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Zinc binding site 8 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1211

b:30.5
occ:1.00
 OD1 B:ASP134 2.2 34.9 1.0
O B:HOH1298 2.3 28.3 1.0
OD2 B:ASP134 2.7 34.4 1.0
CG B:ASP134 2.7 35.3 1.0
O B:HOH1323 2.9 31.6 1.0
CB B:ASP134 4.2 35.4 1.0
O B:HOH1343 4.2 55.4 1.0
CG2 B:THR87 4.5 19.6 1.0
CZ3 B:TRP135 4.7 42.6 1.0
CE3 B:TRP135 4.7 42.4 1.0

Zinc binding site 9 out of 10 in 2d0w

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Zinc binding site 9 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1218

b:42.0
occ:1.00
 ND1 B:HIS106 2.2 19.6 1.0
OD1 B:ASP109 2.2 36.3 1.0
O B:HOH1410 2.7 42.8 1.0
CG B:ASP109 3.1 32.6 1.0
CG B:HIS106 3.2 18.6 1.0
CE1 B:HIS106 3.2 20.0 1.0
CB B:ASP109 3.3 28.7 1.0
CB B:HIS106 3.4 17.2 1.0
CA B:HIS106 3.9 15.9 1.0
O B:HOH1260 4.1 27.4 1.0
O B:HOH1291 4.2 41.6 1.0
NE2 B:HIS106 4.3 20.4 1.0
CD2 B:HIS106 4.3 19.1 1.0
OD2 B:ASP109 4.3 36.6 1.0
O B:PRO105 4.3 15.4 1.0
O B:HIS106 4.7 15.4 1.0
C B:HIS106 4.8 16.3 1.0
CA B:ASP109 4.8 26.4 1.0
N B:HIS106 4.9 16.4 1.0
O B:HOH1398 5.0 32.9 1.0

Zinc binding site 10 out of 10 in 2d0w

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Zinc binding site 10 out of 10 in the Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of Cytochrome Cl From Hyphomicrobium Denitrificans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1219

b:21.3
occ:1.00
 OE2 B:GLU3 1.9 24.2 1.0
CD B:GLU3 2.8 23.4 1.0
OE1 B:GLU3 3.1 25.1 1.0
O B:HOH1322 3.4 33.7 1.0
CG B:GLU3 4.2 22.6 1.0
O B:HOH1221 4.3 15.5 1.0
CB B:GLU3 4.7 23.4 1.0
CA B:GLU3 4.9 23.1 1.0
CE B:LYS89 5.0 22.9 1.0

Reference:

M.Nojiri, D.Hira, K.Yamaguchi, T.Okajima, K.Tanizawa, S.Suzuki. Crystal Structures of Cytochrome C(L) and Methanol Dehydrogenase From Hyphomicrobium Denitrificans: Structural and Mechanistic Insights Into Interactions Between the Two Proteins Biochemistry V. 45 3481 2006.
ISSN: ISSN 0006-2960
PubMed: 16533029
DOI: 10.1021/BI051877J
Page generated: Wed Dec 16 03:20:34 2020

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