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Zinc in PDB 2vkr: 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin

Protein crystallography data

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr was solved by C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.48 / 2.01
Space group P 31
Cell size a, b, c (Å), α, β, γ (°) 117.500, 117.500, 50.900, 90.00, 90.00, 120.00
R / Rfree (%) 22 / 27.3

Other elements in 2vkr:

The structure of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin also contains other interesting chemical elements:

Iron (Fe) 49 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin (pdb code 2vkr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin, PDB code: 2vkr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 2vkr

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Zinc binding site 1 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn106

b:0.2
occ:1.00
 NE2 A:HIS19 1.8 24.6 1.0
ND1 A:HIS16 1.8 26.2 1.0
OD1 A:ASP76 1.8 17.5 1.0
ND1 A:HIS34 1.9 19.7 1.0
CE1 A:HIS19 2.6 27.1 1.0
CE1 A:HIS16 2.7 30.0 1.0
CE1 A:HIS34 2.7 18.0 1.0
CG A:ASP76 2.7 28.0 1.0
CG A:HIS16 2.9 30.4 1.0
CD2 A:HIS19 2.9 26.8 1.0
OD2 A:ASP76 3.0 24.9 1.0
CG A:HIS34 3.0 21.2 1.0
CB A:HIS16 3.4 31.7 1.0
CB A:HIS34 3.6 22.7 1.0
ND1 A:HIS19 3.8 25.4 1.0
NE2 A:HIS16 3.8 29.1 1.0
NE2 A:HIS34 3.9 20.0 1.0
CD2 A:HIS16 4.0 29.9 1.0
CG A:HIS19 4.0 26.3 1.0
CD2 A:HIS34 4.1 20.0 1.0
O A:HIS16 4.1 29.4 1.0
CB A:ASP76 4.1 21.0 1.0
CZ A:PHE42 4.3 19.4 1.0
CE2 A:PHE42 4.5 22.1 1.0
C A:HIS16 4.6 30.0 1.0
CD A:PRO77 4.6 20.8 1.0
CA A:HIS16 4.6 30.7 1.0
CA A:HIS34 4.8 24.2 1.0
CA A:ASP76 4.9 22.3 1.0

Zinc binding site 2 out of 7 in 2vkr

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Zinc binding site 2 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn106

b:0.5
occ:1.00
 NE2 B:HIS19 1.8 24.6 1.0
OD1 B:ASP76 1.8 17.5 1.0
ND1 B:HIS16 1.8 26.1 1.0
ND1 B:HIS34 1.9 19.7 1.0
CE1 B:HIS19 2.6 27.1 1.0
CE1 B:HIS16 2.6 29.9 1.0
CE1 B:HIS34 2.7 18.0 1.0
CG B:ASP76 2.8 28.0 1.0
CG B:HIS16 2.9 30.4 1.0
CD2 B:HIS19 3.0 26.8 1.0
CG B:HIS34 3.0 21.2 1.0
OD2 B:ASP76 3.1 24.8 1.0
CB B:HIS16 3.5 31.7 1.0
CB B:HIS34 3.6 22.7 1.0
ND1 B:HIS19 3.8 25.4 1.0
NE2 B:HIS16 3.8 29.1 1.0
NE2 B:HIS34 3.9 19.9 1.0
CD2 B:HIS16 4.0 29.9 1.0
CG B:HIS19 4.0 26.3 1.0
CD2 B:HIS34 4.1 20.0 1.0
CB B:ASP76 4.1 21.0 1.0
O B:HIS16 4.2 29.4 1.0
CZ B:PHE42 4.3 19.5 1.0
CE2 B:PHE42 4.6 22.1 1.0
CD B:PRO77 4.7 20.9 1.0
CA B:HIS16 4.7 30.7 1.0
C B:HIS16 4.7 30.0 1.0
CA B:ASP76 4.9 22.4 1.0
CA B:HIS34 4.9 24.2 1.0
CG2 B:VAL21 4.9 27.1 1.0

Zinc binding site 3 out of 7 in 2vkr

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Zinc binding site 3 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn106

b:3.3
occ:1.00
 NE2 C:HIS19 1.8 24.5 1.0
ND1 C:HIS16 1.8 26.2 1.0
OD1 C:ASP76 1.8 17.6 1.0
ND1 C:HIS34 1.9 19.7 1.0
CE1 C:HIS19 2.6 27.0 1.0
CE1 C:HIS16 2.7 30.0 1.0
CE1 C:HIS34 2.7 17.9 1.0
CG C:ASP76 2.7 28.0 1.0
CD2 C:HIS19 2.9 26.8 1.0
CG C:HIS16 2.9 30.4 1.0
OD2 C:ASP76 3.0 24.9 1.0
CG C:HIS34 3.0 21.1 1.0
CB C:HIS16 3.5 31.7 1.0
CB C:HIS34 3.6 22.7 1.0
ND1 C:HIS19 3.8 25.4 1.0
NE2 C:HIS16 3.8 29.1 1.0
NE2 C:HIS34 3.9 20.0 1.0
CG C:HIS19 4.0 26.3 1.0
CD2 C:HIS16 4.0 30.0 1.0
CD2 C:HIS34 4.1 20.0 1.0
CZ C:PHE42 4.1 19.5 1.0
CB C:ASP76 4.1 21.0 1.0
O C:HIS16 4.3 29.3 1.0
CD C:PRO77 4.5 20.8 1.0
CE2 C:PHE42 4.5 22.1 1.0
C C:HIS16 4.7 30.0 1.0
CA C:HIS16 4.7 30.7 1.0
CA C:ASP76 4.8 22.3 1.0
CA C:HIS34 4.9 24.2 1.0

Zinc binding site 4 out of 7 in 2vkr

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Zinc binding site 4 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn106

b:0.5
occ:1.00
 NE2 D:HIS19 1.8 24.6 1.0
ND1 D:HIS16 1.8 26.0 1.0
OD1 D:ASP76 1.8 17.4 1.0
ND1 D:HIS34 1.9 19.8 1.0
CE1 D:HIS19 2.6 27.1 1.0
CE1 D:HIS16 2.7 30.0 1.0
CE1 D:HIS34 2.7 18.0 1.0
CG D:ASP76 2.7 28.1 1.0
CG D:HIS16 2.9 30.4 1.0
CD2 D:HIS19 3.0 26.8 1.0
OD2 D:ASP76 3.0 24.9 1.0
CG D:HIS34 3.0 21.2 1.0
CB D:HIS16 3.5 31.7 1.0
CB D:HIS34 3.5 22.7 1.0
ND1 D:HIS19 3.8 25.4 1.0
NE2 D:HIS16 3.8 29.1 1.0
NE2 D:HIS34 3.9 20.0 1.0
CD2 D:HIS16 4.0 30.0 1.0
CG D:HIS19 4.0 26.3 1.0
CD2 D:HIS34 4.1 20.0 1.0
CB D:ASP76 4.2 21.0 1.0
O D:HIS16 4.2 29.4 1.0
CZ D:PHE42 4.3 19.4 1.0
CD D:PRO77 4.5 20.8 1.0
CE2 D:PHE42 4.6 22.1 1.0
C D:HIS16 4.7 30.0 1.0
CA D:HIS16 4.7 30.7 1.0
CG2 D:VAL21 4.7 27.1 1.0
CA D:HIS34 4.8 24.3 1.0
CA D:ASP76 4.9 22.3 1.0

Zinc binding site 5 out of 7 in 2vkr

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Zinc binding site 5 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn106

b:24.1
occ:1.00
 NE2 E:HIS19 1.8 24.7 1.0
OD1 E:ASP76 1.8 45.4 1.0
ND1 E:HIS16 1.8 26.3 1.0
ND1 E:HIS34 1.9 19.8 1.0
CE1 E:HIS19 2.6 27.2 1.0
CE1 E:HIS16 2.7 30.1 1.0
CE1 E:HIS34 2.7 18.0 1.0
CG E:ASP76 2.7 55.2 1.0
CG E:HIS16 2.9 30.4 1.0
CD2 E:HIS19 2.9 26.9 1.0
OD2 E:ASP76 3.0 65.0 1.0
CG E:HIS34 3.0 21.2 1.0
CB E:HIS34 3.5 22.7 1.0
CB E:HIS16 3.5 31.8 1.0
ND1 E:HIS19 3.8 25.4 1.0
NE2 E:HIS16 3.8 29.3 1.0
NE2 E:HIS34 3.9 20.0 1.0
CG E:HIS19 4.0 26.4 1.0
CD2 E:HIS16 4.0 29.9 1.0
O E:HIS16 4.0 29.5 1.0
CD2 E:HIS34 4.1 20.0 1.0
CB E:ASP76 4.1 48.7 1.0
CE2 E:PHE42 4.2 22.1 1.0
CZ E:PHE42 4.2 19.4 1.0
CD E:PRO77 4.4 48.4 1.0
C E:HIS16 4.5 30.1 1.0
CA E:HIS16 4.6 30.7 1.0
CA E:HIS34 4.7 24.3 1.0
NE2 E:GLN17 4.7 55.4 1.0
CA E:ASP76 5.0 46.4 1.0

Zinc binding site 6 out of 7 in 2vkr

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Zinc binding site 6 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn106

b:8.1
occ:1.00
 NE2 F:HIS19 1.8 24.6 1.0
OD1 F:ASP76 1.8 17.5 1.0
ND1 F:HIS16 1.8 26.2 1.0
ND1 F:HIS34 1.9 19.7 1.0
CE1 F:HIS19 2.6 27.1 1.0
CE1 F:HIS16 2.6 30.0 1.0
CE1 F:HIS34 2.7 18.1 1.0
CG F:ASP76 2.8 28.0 1.0
CD2 F:HIS19 2.9 26.8 1.0
CG F:HIS16 3.0 30.4 1.0
OD2 F:ASP76 3.0 24.9 1.0
CG F:HIS34 3.0 21.2 1.0
CB F:HIS16 3.5 31.7 1.0
CB F:HIS34 3.6 22.8 1.0
ND1 F:HIS19 3.8 25.4 1.0
NE2 F:HIS16 3.8 29.1 1.0
NE2 F:HIS34 3.9 20.1 1.0
CD2 F:HIS16 4.0 29.9 1.0
CG F:HIS19 4.0 26.3 1.0
CD2 F:HIS34 4.1 20.0 1.0
CB F:ASP76 4.1 21.0 1.0
O F:HIS16 4.2 29.5 1.0
CZ F:PHE42 4.3 19.4 1.0
CD F:PRO77 4.4 20.8 1.0
CE2 F:PHE42 4.6 22.1 1.0
C F:HIS16 4.6 30.1 1.0
CA F:HIS16 4.7 30.7 1.0
CG2 F:VAL21 4.7 27.2 1.0
CA F:ASP76 4.8 22.4 1.0
CA F:HIS34 4.9 24.3 1.0

Zinc binding site 7 out of 7 in 2vkr

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Zinc binding site 7 out of 7 in the 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of 3FE-4S, 4FE-4S Plus Zn Acidianus Ambivalens Ferredoxin within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn106

b:5.1
occ:1.00
 NE2 G:HIS19 1.8 24.6 1.0
OD1 G:ASP76 1.8 17.5 1.0
ND1 G:HIS16 1.8 26.2 1.0
ND1 G:HIS34 1.9 19.8 1.0
CE1 G:HIS19 2.6 27.1 1.0
CE1 G:HIS16 2.7 30.1 1.0
CE1 G:HIS34 2.7 18.0 1.0
CG G:ASP76 2.8 28.0 1.0
CG G:HIS16 2.9 30.4 1.0
CD2 G:HIS19 2.9 26.9 1.0
CG G:HIS34 3.1 21.2 1.0
OD2 G:ASP76 3.1 24.9 1.0
CB G:HIS16 3.4 31.7 1.0
CB G:HIS34 3.6 22.6 1.0
ND1 G:HIS19 3.8 25.4 1.0
NE2 G:HIS16 3.8 29.1 1.0
NE2 G:HIS34 3.9 20.0 1.0
CD2 G:HIS16 4.0 29.9 1.0
CG G:HIS19 4.0 26.4 1.0
CD2 G:HIS34 4.1 20.0 1.0
CB G:ASP76 4.1 21.0 1.0
O G:HIS16 4.2 29.4 1.0
CZ G:PHE42 4.4 19.4 1.0
CD G:PRO77 4.4 20.8 1.0
C G:HIS16 4.6 30.1 1.0
CA G:HIS16 4.6 30.7 1.0
CE2 G:PHE42 4.8 22.1 1.0
CA G:ASP76 4.8 22.3 1.0
CA G:HIS34 4.8 24.3 1.0

Reference:

C.Frazao, D.Aragao, R.Coelho, S.S.Leal, C.M.Gomes, M.Teixeira, M.A.Carrondo. Crystallographic Analysis of the Intact Metal Centres [3FE-4S](1+/0) and [4FE-4S](2+/1+) in A Zn(2+) -Containing Ferredoxin. Febs Lett. V. 582 763 2008.
ISSN: ISSN 0014-5793
PubMed: 18258200
DOI: 10.1016/J.FEBSLET.2008.01.041
Page generated: Thu Oct 17 04:20:27 2024

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