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Zinc in PDB 2vus: Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex

Protein crystallography data

The structure of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex, PDB code: 2vus was solved by M.Kotaka, C.Johnson, H.K.Lamb, A.R.Hawkins, J.Ren, D.K.Stammers, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.97 / 2.6
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 228.788, 228.788, 222.296, 90.00, 90.00, 120.00
R / Rfree (%) 24.2 / 30.6

Other elements in 2vus:

The structure of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex also contains other interesting chemical elements:

Chlorine (Cl) 7 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex (pdb code 2vus). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex, PDB code: 2vus:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2vus

Go back to Zinc Binding Sites List in 2vus
Zinc binding site 1 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1713

b:38.2
occ:1.00
 SG I:CYS676 2.1 31.3 1.0
SG I:CYS697 2.3 15.3 1.0
SG I:CYS673 2.4 34.2 1.0
SG I:CYS694 2.5 29.9 1.0
CB I:CYS697 3.0 10.1 1.0
CB I:CYS676 3.2 30.1 1.0
CB I:CYS694 3.4 28.4 1.0
NH2 I:ARG708 3.5 35.1 1.0
CB I:CYS673 3.5 30.1 1.0
N I:CYS676 3.6 33.8 1.0
N I:CYS694 3.8 39.5 1.0
CA I:CYS676 3.9 34.9 1.0
CG2 I:THR678 4.1 19.9 1.0
N I:CYS697 4.1 14.8 1.0
CA I:CYS694 4.1 35.1 1.0
CA I:CYS697 4.2 11.9 1.0
O A:HOH2091 4.4 21.1 1.0
CB I:ASN675 4.5 33.4 1.0
CZ I:ARG708 4.6 36.1 1.0
O I:CYS694 4.7 31.0 1.0
ND2 I:ASN675 4.7 32.3 1.0
C I:CYS676 4.7 27.0 1.0
C I:ASN675 4.7 29.6 1.0
C I:CYS694 4.8 30.5 1.0
N I:PHE677 4.9 31.4 1.0
CA I:CYS673 4.9 31.8 1.0
C I:LEU693 4.9 33.7 1.0

Zinc binding site 2 out of 8 in 2vus

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Zinc binding site 2 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1713

b:40.6
occ:1.00
 SG J:CYS676 2.2 31.3 1.0
SG J:CYS694 2.2 32.4 1.0
SG J:CYS697 2.4 25.0 1.0
SG J:CYS673 2.4 33.4 1.0
CB J:CYS673 3.3 44.4 1.0
CB J:CYS697 3.3 13.1 1.0
CB J:CYS676 3.4 38.7 1.0
CB J:CYS694 3.4 26.8 1.0
N J:CYS676 3.7 45.6 1.0
N J:CYS694 3.8 29.9 1.0
CA J:CYS676 4.1 40.6 1.0
CG2 J:THR678 4.1 25.3 1.0
N J:CYS697 4.2 22.2 1.0
CA J:CYS694 4.2 25.9 1.0
O B:HOH2174 4.3 11.8 1.0
CA J:CYS697 4.4 22.1 1.0
ND2 J:ASN675 4.6 24.6 1.0
CB J:ASN675 4.6 28.8 1.0
CA J:CYS673 4.7 44.0 1.0
C J:CYS676 4.8 35.8 1.0
C J:CYS694 4.8 25.2 1.0
N J:PHE677 4.9 35.8 1.0
C J:ASN675 4.9 42.3 1.0
CD2 J:LEU693 4.9 16.6 1.0
NH1 J:ARG708 4.9 44.2 1.0
O J:CYS694 4.9 14.8 1.0
C J:LEU693 4.9 21.3 1.0

Zinc binding site 3 out of 8 in 2vus

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Zinc binding site 3 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1712

b:30.4
occ:1.00
 SG K:CYS676 2.3 29.4 1.0
SG K:CYS697 2.3 29.4 1.0
SG K:CYS673 2.4 42.9 1.0
SG K:CYS694 2.5 32.5 1.0
CB K:CYS697 3.2 7.5 1.0
CB K:CYS694 3.3 30.9 1.0
CB K:CYS673 3.3 52.8 1.0
CB K:CYS676 3.6 39.8 1.0
N K:CYS694 3.7 22.7 1.0
N K:CYS676 3.7 40.2 1.0
CA K:CYS694 4.1 22.4 1.0
N K:CYS697 4.1 13.1 1.0
CG2 K:THR678 4.2 20.6 1.0
CA K:CYS676 4.2 39.4 1.0
O C:HOH2181 4.3 9.8 1.0
CA K:CYS697 4.3 23.4 1.0
NH2 K:ARG708 4.3 22.5 1.0
CB K:ASN675 4.4 41.1 1.0
O K:CYS694 4.7 34.6 1.0
CA K:CYS673 4.7 47.6 1.0
C K:CYS694 4.7 29.8 1.0
C K:ASN675 4.8 36.3 1.0
C K:LEU693 4.9 23.3 1.0
N K:PHE677 4.9 45.1 1.0
C K:CYS676 4.9 38.3 1.0
CA K:ASN675 5.0 33.7 1.0

Zinc binding site 4 out of 8 in 2vus

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Zinc binding site 4 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1713

b:36.3
occ:1.00
 SG L:CYS676 2.1 34.5 1.0
SG L:CYS697 2.2 38.0 1.0
SG L:CYS673 2.4 44.7 1.0
SG L:CYS694 2.5 44.1 1.0
CB L:CYS697 3.1 13.0 1.0
CB L:CYS673 3.2 31.6 1.0
CB L:CYS694 3.5 36.8 1.0
CB L:CYS676 3.5 29.6 1.0
N L:CYS676 3.8 47.7 1.0
N L:CYS694 3.8 39.3 1.0
CG2 L:THR678 3.9 33.4 1.0
N L:CYS697 4.1 24.4 1.0
NH1 L:ARG708 4.1 37.1 1.0
CA L:CYS694 4.2 36.5 1.0
CA L:CYS697 4.2 26.5 1.0
CA L:CYS676 4.3 32.3 1.0
O D:HOH2181 4.4 8.5 1.0
CB L:ASN675 4.5 49.0 1.0
CA L:CYS673 4.7 45.3 1.0
C L:CYS694 4.8 39.7 1.0
N L:PHE677 4.9 42.3 1.0
C L:ASN675 4.9 48.4 1.0
C L:LEU693 4.9 36.7 1.0
C L:CYS676 4.9 36.1 1.0
O L:CYS694 5.0 42.8 1.0
CB L:THR678 5.0 45.0 1.0

Zinc binding site 5 out of 8 in 2vus

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Zinc binding site 5 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1713

b:43.9
occ:1.00
 SG M:CYS676 2.2 31.3 1.0
SG M:CYS697 2.2 37.8 1.0
SG M:CYS694 2.2 31.8 1.0
SG M:CYS673 2.3 31.0 1.0
CB M:CYS673 3.3 54.3 1.0
CB M:CYS676 3.3 32.5 1.0
CB M:CYS697 3.3 23.4 1.0
CB M:CYS694 3.5 23.5 1.0
N M:CYS676 3.6 32.9 1.0
N M:CYS694 3.9 39.8 1.0
NH2 M:ARG708 4.0 4.2 1.0
CA M:CYS676 4.0 37.9 1.0
CG2 M:THR678 4.1 12.5 1.0
N M:CYS697 4.3 20.2 1.0
CA M:CYS694 4.3 36.0 1.0
CA M:CYS697 4.4 19.4 1.0
CB M:ASN675 4.5 25.2 1.0
C M:CYS676 4.7 39.3 1.0
N M:PHE677 4.7 41.9 1.0
C M:ASN675 4.7 28.4 1.0
CA M:CYS673 4.7 56.5 1.0
OD1 M:ASN675 4.8 27.3 1.0
CZ M:ARG708 4.9 24.2 1.0
CB M:THR678 4.9 35.3 1.0
NE M:ARG708 4.9 32.5 1.0
C M:CYS694 4.9 32.2 1.0
N M:THR678 5.0 41.9 1.0

Zinc binding site 6 out of 8 in 2vus

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Zinc binding site 6 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1713

b:34.4
occ:1.00
 SG N:CYS694 2.2 32.6 1.0
SG N:CYS676 2.3 31.0 1.0
SG N:CYS697 2.4 29.7 1.0
SG N:CYS673 2.4 38.2 1.0
CB N:CYS697 3.1 12.2 1.0
CB N:CYS673 3.4 37.1 1.0
CB N:CYS694 3.4 12.3 1.0
CB N:CYS676 3.6 23.4 1.0
NH2 N:ARG708 3.7 25.5 1.0
N N:CYS694 3.8 40.6 1.0
N N:CYS676 3.8 34.7 1.0
CG2 N:THR678 4.0 5.8 1.0
N N:CYS697 4.0 8.6 1.0
CA N:CYS694 4.1 35.2 1.0
CA N:CYS697 4.2 15.2 1.0
CA N:CYS676 4.3 32.6 1.0
O N:CYS694 4.6 27.0 1.0
CB N:ASN675 4.7 34.6 1.0
C N:CYS694 4.7 34.0 1.0
CZ N:ARG708 4.8 26.7 1.0
CA N:CYS673 4.8 40.8 1.0
C N:LEU693 4.8 35.6 1.0
C N:CYS676 4.9 31.0 1.0
CB N:THR678 4.9 24.1 1.0
NE N:ARG708 4.9 29.2 1.0
C N:ASN675 4.9 33.6 1.0
N N:PHE677 5.0 37.9 1.0

Zinc binding site 7 out of 8 in 2vus

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Zinc binding site 7 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


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 Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn1712

b:57.2
occ:1.00
 SG O:CYS694 2.3 34.3 1.0
SG O:CYS676 2.4 32.0 1.0
SG O:CYS697 2.4 37.0 1.0
SG O:CYS673 2.5 42.7 1.0
CB O:CYS697 3.2 14.0 1.0
CB O:CYS694 3.3 21.8 1.0
CB O:CYS673 3.4 54.2 1.0
CB O:CYS676 3.4 9.5 1.0
N O:CYS694 3.6 38.5 1.0
N O:CYS676 3.8 34.9 1.0
CG2 O:THR678 3.9 14.7 1.0
N O:CYS697 4.0 23.2 1.0
CA O:CYS694 4.0 37.0 1.0
CA O:CYS676 4.2 30.8 1.0
CA O:CYS697 4.2 35.4 1.0
NH2 O:ARG708 4.3 18.8 1.0
O G:HOH2204 4.4 23.4 1.0
O O:CYS694 4.5 36.8 1.0
C O:CYS694 4.6 36.9 1.0
CB O:ASN675 4.6 41.4 1.0
C O:LEU693 4.7 32.3 1.0
C O:CYS676 4.8 31.3 1.0
N O:PHE677 4.8 39.7 1.0
NE O:ARG708 4.8 38.4 1.0
CA O:CYS673 4.9 44.4 1.0
C O:ASN675 4.9 36.2 1.0
CB O:THR678 5.0 21.6 1.0
N O:THR678 5.0 32.3 1.0
CA O:LEU693 5.0 27.0 1.0

Zinc binding site 8 out of 8 in 2vus

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Zinc binding site 8 out of 8 in the Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Unliganded Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1713

b:34.5
occ:1.00
 SG P:CYS673 2.1 46.2 1.0
SG P:CYS676 2.2 31.2 1.0
SG P:CYS697 2.2 30.0 1.0
SG P:CYS694 2.3 32.0 1.0
CB P:CYS697 3.0 9.5 1.0
CB P:CYS673 3.2 48.0 1.0
CB P:CYS694 3.3 29.7 1.0
CB P:CYS676 3.4 27.1 1.0
N P:CYS676 3.5 30.1 1.0
N P:CYS694 3.8 31.6 1.0
CA P:CYS676 4.0 41.1 1.0
CA P:CYS694 4.2 34.3 1.0
NH2 P:ARG708 4.2 10.8 1.0
CA P:CYS697 4.2 18.1 1.0
N P:CYS697 4.3 23.1 1.0
CG2 P:THR678 4.4 5.0 1.0
CB P:ASN675 4.4 44.1 1.0
ND2 P:ASN675 4.4 52.5 1.0
NE P:ARG708 4.4 24.2 1.0
C P:ASN675 4.6 27.2 1.0
CA P:CYS673 4.6 47.7 1.0
N P:PHE677 4.6 38.2 1.0
C P:CYS676 4.7 38.9 1.0
CZ P:ARG708 4.8 23.1 1.0
CA P:ASN675 4.9 32.3 1.0
C P:CYS694 4.9 36.6 1.0
N P:ASN675 4.9 39.5 1.0
CG P:ASN675 5.0 46.5 1.0
C P:LEU693 5.0 31.3 1.0

Reference:

M.Kotaka, C.Johnson, H.K.Lamb, A.R.Hawkins, J.Ren, D.K.Stammers. Structural Analysis of the Recognition of the Negative Regulator Nmra and Dna By the Zinc Finger From the Gata-Type Transcription Factor Area. J.Mol.Biol. V. 381 373 2008.
ISSN: ISSN 0022-2836
PubMed: 18602114
DOI: 10.1016/J.JMB.2008.05.077
Page generated: Thu Oct 17 04:34:22 2024

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