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Zinc in PDB 2vuu: Crystal Structure of Nadp-Bound Nmra-Area Zinc Finger Complex

Protein crystallography data

The structure of Crystal Structure of Nadp-Bound Nmra-Area Zinc Finger Complex, PDB code: 2vuu 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) 29.86 / 2.8
Space group H 3
Cell size a, b, c (Å), α, β, γ (°) 231.730, 231.730, 223.450, 90.00, 90.00, 120.00
R / Rfree (%) 23.2 / 28.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Nadp-Bound Nmra-Area Zinc Finger Complex (pdb code 2vuu). 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 Nadp-Bound Nmra-Area Zinc Finger Complex, PDB code: 2vuu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 2vuu

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Zinc binding site 1 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn1713

b:58.9
occ:1.00
 SG I:CYS694 2.0 45.8 1.0
SG I:CYS676 2.2 51.0 1.0
SG I:CYS697 2.3 47.3 1.0
SG I:CYS673 2.3 45.3 1.0
CB I:CYS673 3.1 66.0 1.0
CB I:CYS697 3.3 53.1 1.0
CB I:CYS694 3.3 50.1 1.0
CB I:CYS676 3.4 57.1 1.0
N I:CYS676 3.5 60.6 1.0
NH2 I:ARG708 3.6 59.8 1.0
N I:CYS694 3.9 52.7 1.0
CA I:CYS676 4.0 60.1 1.0
CG2 I:THR678 4.2 40.0 1.0
CA I:CYS694 4.2 50.4 1.0
N I:CYS697 4.2 46.2 1.0
CB I:ASN675 4.3 58.9 1.0
CA I:CYS697 4.4 43.1 1.0
N I:PHE677 4.5 52.4 1.0
CA I:CYS673 4.6 63.2 1.0
C I:ASN675 4.6 60.7 1.0
C I:CYS676 4.6 56.2 1.0
ND2 I:ASN675 4.7 62.6 1.0
CZ I:ARG708 4.7 45.4 1.0
N I:ASN675 4.8 64.3 1.0
CA I:ASN675 4.8 61.3 1.0
NE I:ARG708 4.9 31.3 1.0
N I:THR678 4.9 46.1 1.0
C I:CYS694 4.9 48.4 1.0

Zinc binding site 2 out of 8 in 2vuu

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Zinc binding site 2 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn1713

b:57.8
occ:1.00
 SG J:CYS676 2.1 61.8 1.0
SG J:CYS694 2.2 60.4 1.0
SG J:CYS673 2.2 61.4 1.0
SG J:CYS697 2.3 42.6 1.0
CB J:CYS673 3.1 63.9 1.0
CB J:CYS694 3.3 60.6 1.0
CB J:CYS697 3.4 47.8 1.0
CB J:CYS676 3.4 62.4 1.0
N J:CYS676 3.5 58.9 1.0
N J:CYS694 3.9 54.6 1.0
CG2 J:THR678 4.0 45.4 1.0
CA J:CYS676 4.0 59.6 1.0
CA J:CYS694 4.2 57.8 1.0
CB J:ASN675 4.3 55.1 1.0
N J:CYS697 4.3 50.1 1.0
CA J:CYS697 4.5 54.1 1.0
CA J:CYS673 4.5 69.4 1.0
N J:PHE677 4.6 60.5 1.0
C J:ASN675 4.6 61.9 1.0
C J:CYS676 4.6 59.9 1.0
N J:ASN675 4.7 66.0 1.0
CA J:ASN675 4.8 61.5 1.0
C J:CYS673 4.8 67.0 1.0
N J:THR678 4.9 50.8 1.0
CB J:THR678 4.9 45.6 1.0
O J:CYS673 4.9 65.7 1.0
NE J:ARG708 4.9 43.6 1.0
C J:CYS694 5.0 58.2 1.0

Zinc binding site 3 out of 8 in 2vuu

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Zinc binding site 3 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn1713

b:66.8
occ:1.00
 SG K:CYS694 1.7 46.7 1.0
SG K:CYS673 2.1 64.1 1.0
SG K:CYS697 2.2 59.6 1.0
SG K:CYS676 2.3 43.4 1.0
CB K:CYS697 3.0 35.4 1.0
CB K:CYS673 3.2 70.9 1.0
CB K:CYS676 3.3 45.1 1.0
N K:CYS676 3.3 58.1 1.0
CB K:CYS694 3.4 59.2 1.0
N K:CYS694 3.8 59.0 1.0
CA K:CYS676 3.8 55.1 1.0
CB K:ASN675 4.0 61.6 1.0
NH2 K:ARG708 4.1 54.8 1.0
N K:CYS697 4.2 49.1 1.0
CA K:CYS697 4.2 48.5 1.0
CA K:CYS694 4.2 60.4 1.0
C K:ASN675 4.4 64.5 1.0
N K:PHE677 4.5 59.2 1.0
CA K:ASN675 4.5 63.5 1.0
CA K:CYS673 4.5 70.7 1.0
OD1 K:ASN675 4.6 48.4 1.0
N K:ASN675 4.6 64.1 1.0
CG2 K:THR678 4.6 38.3 1.0
C K:CYS676 4.6 57.9 1.0
CG K:ASN675 4.7 57.7 1.0
C K:CYS673 4.9 68.2 1.0
C K:LEU693 4.9 56.6 1.0
C K:CYS694 5.0 56.5 1.0

Zinc binding site 4 out of 8 in 2vuu

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Zinc binding site 4 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn1713

b:58.2
occ:1.00
 SG L:CYS697 1.8 77.5 1.0
SG L:CYS676 2.1 50.2 1.0
SG L:CYS694 2.3 74.7 1.0
SG L:CYS673 2.3 44.9 1.0
CB L:CYS694 2.4 44.9 1.0
CB L:CYS673 3.0 64.5 1.0
CB L:CYS697 3.2 63.8 1.0
N L:CYS694 3.4 50.8 1.0
CA L:CYS694 3.5 48.5 1.0
CB L:CYS676 3.6 38.5 1.0
N L:CYS676 3.8 53.9 1.0
CG2 L:THR678 3.9 31.8 1.0
N L:CYS697 4.3 55.8 1.0
CA L:CYS676 4.3 51.1 1.0
CA L:CYS697 4.4 64.2 1.0
C L:CYS694 4.5 48.6 1.0
CA L:CYS673 4.5 68.5 1.0
CB L:ASN675 4.5 50.5 1.0
NH2 L:ARG708 4.6 52.8 1.0
C L:LEU693 4.6 49.4 1.0
N L:PHE677 4.7 58.2 1.0
O L:CYS694 4.7 40.7 1.0
CB L:THR678 4.7 48.2 1.0
N L:THR678 4.8 54.3 1.0
C L:CYS676 4.8 54.3 1.0
N L:ASN675 4.9 65.5 1.0
C L:ASN675 4.9 54.4 1.0

Zinc binding site 5 out of 8 in 2vuu

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Zinc binding site 5 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn1712

b:48.1
occ:1.00
 SG M:CYS693 2.0 50.7 1.0
SG M:CYS675 2.3 39.3 1.0
SG M:CYS696 2.4 53.0 1.0
SG M:CYS672 2.5 53.0 1.0
CB M:CYS696 3.2 50.4 1.0
CB M:CYS672 3.2 66.5 1.0
CB M:CYS693 3.3 44.8 1.0
CB M:CYS675 3.6 45.1 1.0
N M:CYS675 3.7 53.0 1.0
N M:CYS693 3.9 47.5 1.0
NH2 M:ARG707 4.0 37.1 1.0
CG2 M:THR677 4.1 36.4 1.0
N M:CYS696 4.1 44.8 1.0
CA M:CYS693 4.2 42.0 1.0
CA M:CYS675 4.2 53.3 1.0
CA M:CYS696 4.3 42.9 1.0
CB M:ASN674 4.5 47.8 1.0
NE M:ARG707 4.6 16.1 1.0
CA M:CYS672 4.7 70.7 1.0
CZ M:ARG707 4.8 31.0 1.0
N M:PHE676 4.8 57.4 1.0
C M:ASN674 4.8 47.3 1.0
C M:CYS693 4.8 39.7 1.0
C M:CYS675 4.9 56.2 1.0
O M:CYS693 4.9 44.1 1.0
CB M:THR677 5.0 41.5 1.0
CA M:ASN674 5.0 48.9 1.0

Zinc binding site 6 out of 8 in 2vuu

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Zinc binding site 6 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn1713

b:53.5
occ:1.00
 SG N:CYS676 2.0 52.5 1.0
SG N:CYS697 2.1 44.7 1.0
SG N:CYS673 2.3 58.4 1.0
SG N:CYS694 2.5 34.5 1.0
CB N:CYS673 3.1 54.9 1.0
CB N:CYS694 3.2 41.5 1.0
CB N:CYS676 3.3 59.8 1.0
CB N:CYS697 3.5 41.4 1.0
N N:CYS676 3.6 57.7 1.0
CG2 N:THR678 3.6 46.1 1.0
N N:CYS694 3.9 42.3 1.0
CA N:CYS676 3.9 59.6 1.0
CA N:CYS694 4.2 45.5 1.0
NH2 N:ARG708 4.3 36.0 1.0
N N:CYS697 4.3 36.3 1.0
C N:CYS676 4.5 60.2 1.0
CA N:CYS697 4.5 37.3 1.0
CB N:ASN675 4.5 52.6 1.0
CA N:CYS673 4.6 64.5 1.0
N N:PHE677 4.7 61.4 1.0
CB N:THR678 4.7 44.9 1.0
N N:THR678 4.7 54.0 1.0
C N:ASN675 4.7 55.9 1.0
C N:CYS694 4.9 53.9 1.0

Zinc binding site 7 out of 8 in 2vuu

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Zinc binding site 7 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
O:Zn1712

b:53.0
occ:1.00
 SG O:CYS676 2.0 46.1 1.0
SG O:CYS694 2.2 49.6 1.0
SG O:CYS673 2.3 52.5 1.0
SG O:CYS697 2.3 60.1 1.0
CB O:CYS676 3.0 43.3 1.0
CB O:CYS697 3.1 41.7 1.0
CB O:CYS694 3.3 52.9 1.0
CB O:CYS673 3.4 63.0 1.0
N O:CYS676 3.5 50.5 1.0
N O:CYS694 3.8 54.5 1.0
CA O:CYS676 3.8 49.3 1.0
N O:CYS697 4.1 47.7 1.0
CA O:CYS694 4.1 55.2 1.0
CA O:CYS697 4.2 48.1 1.0
CG2 O:THR678 4.3 35.8 1.0
NH2 O:ARG708 4.3 49.4 1.0
C O:CYS676 4.6 52.0 1.0
CB O:ASN675 4.6 56.2 1.0
C O:ASN675 4.7 52.2 1.0
N O:PHE677 4.7 56.2 1.0
C O:CYS694 4.8 54.0 1.0
O O:CYS694 4.8 49.5 1.0
CA O:CYS673 4.8 68.2 1.0
C O:LEU693 4.8 54.1 1.0
NE O:ARG708 5.0 51.4 1.0
N O:ASN675 5.0 66.2 1.0
CA O:ASN675 5.0 55.9 1.0

Zinc binding site 8 out of 8 in 2vuu

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Zinc binding site 8 out of 8 in the Crystal Structure of Nadp-Bound 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 Nadp-Bound Nmra-Area Zinc Finger Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Zn1713

b:47.5
occ:1.00
 SG P:CYS676 2.1 38.2 1.0
SG P:CYS697 2.1 53.5 1.0
SG P:CYS673 2.2 52.6 1.0
SG P:CYS694 2.3 55.0 1.0
CB P:CYS676 2.9 50.7 1.0
CB P:CYS697 3.1 41.2 1.0
CB P:CYS673 3.3 68.0 1.0
N P:CYS676 3.5 43.8 1.0
CB P:CYS694 3.6 54.5 1.0
CA P:CYS676 3.7 52.6 1.0
NH2 P:ARG708 3.9 30.2 1.0
N P:CYS694 4.0 50.2 1.0
N P:CYS697 4.1 34.9 1.0
CA P:CYS697 4.2 40.3 1.0
CA P:CYS694 4.4 52.6 1.0
CG2 P:THR678 4.5 50.3 1.0
NE P:ARG708 4.5 48.4 1.0
N P:PHE677 4.5 60.3 1.0
C P:CYS676 4.5 56.7 1.0
CB P:ASN675 4.6 47.8 1.0
C P:ASN675 4.6 48.0 1.0
CZ P:ARG708 4.7 33.5 1.0
CA P:CYS673 4.7 69.7 1.0
OD1 P:ASN675 4.9 37.2 1.0
CA P:ASN675 5.0 48.6 1.0
O P:CYS694 5.0 61.3 1.0
C P:CYS694 5.0 57.5 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 04:35:31 2024

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