Zinc in PDB 2vut: Crystal Structure of Nad-Bound Nmra-Area Zinc Finger Complex

The structure of Crystal Structure of Nad-Bound Nmra-Area Zinc Finger Complex, PDB code: 2vut 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 / 2.3
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	227.520, 227.520, 222.570, 90.00, 90.00, 120.00
R / Rfree (%)	21.5 / 27.4

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

Chlorine

(Cl)

7 atoms

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

Zinc binding site 1 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ I:Zn1713 b:32.5 occ:1.00 SG I:CYS676 2.1 26.6 1.0 SG I:CYS694 2.2 29.0 1.0 SG I:CYS673 2.4 30.7 1.0 SG I:CYS697 2.4 22.8 1.0 CB I:CYS673 3.2 51.5 1.0 CB I:CYS697 3.2 19.4 1.0 CB I:CYS694 3.3 24.3 1.0 CB I:CYS676 3.5 29.0 1.0 N I:CYS694 3.7 34.1 1.0 N I:CYS676 3.7 31.1 1.0 NH2 I:ARG708 3.9 34.1 1.0 CG2 I:THR678 3.9 17.1 1.0 CA I:CYS694 4.0 23.0 1.0 CA I:CYS676 4.1 33.7 1.0 N I:CYS697 4.2 21.8 1.0 CA I:CYS697 4.4 26.0 1.0 CB I:ASN675 4.4 34.3 1.0 CA I:CYS673 4.7 47.0 1.0 C I:CYS694 4.7 26.6 1.0 C I:CYS676 4.8 35.0 1.0 C I:ASN675 4.8 32.2 1.0 C I:LEU693 4.8 32.3 1.0 N I:PHE677 4.8 32.3 1.0 CZ I:ARG708 4.9 39.0 1.0 O I:CYS694 4.9 29.7 1.0 OD1 I:ASN675 4.9 29.0 1.0 NE I:ARG708 5.0 28.8 1.0 CA I:ASN675 5.0 38.9 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ J:Zn1713 b:38.3 occ:1.00 SG J:CYS676 2.1 33.2 1.0 SG J:CYS694 2.3 33.6 1.0 SG J:CYS697 2.5 24.9 1.0 SG J:CYS673 2.5 39.3 1.0 CB J:CYS673 3.2 47.1 1.0 CB J:CYS694 3.2 38.6 1.0 CB J:CYS697 3.3 25.9 1.0 CB J:CYS676 3.3 19.4 1.0 N J:CYS676 3.7 44.4 1.0 O B:HOH2184 4.0 26.0 1.0 N J:CYS694 4.0 40.3 1.0 CG2 J:THR678 4.0 49.6 1.0 N J:CYS697 4.1 28.9 1.0 CA J:CYS676 4.1 38.1 1.0 CA J:CYS694 4.2 39.9 1.0 CA J:CYS697 4.3 32.6 1.0 NH2 J:ARG708 4.4 52.5 1.0 OD1 J:ASN675 4.7 34.0 1.0 CA J:CYS673 4.7 48.5 1.0 C J:CYS694 4.7 43.0 1.0 O J:CYS694 4.8 45.5 1.0 C J:CYS676 4.8 42.8 1.0 CB J:ASN675 4.8 34.9 1.0 N J:PHE677 4.8 42.2 1.0 C J:ASN675 4.9 49.2 1.0 CB J:THR678 5.0 52.9 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ K:Zn1712 b:27.1 occ:1.00 SG K:CYS694 2.2 29.7 1.0 SG K:CYS676 2.3 37.2 1.0 SG K:CYS673 2.4 35.7 1.0 SG K:CYS697 2.4 25.3 1.0 CB K:CYS694 3.2 21.3 1.0 CB K:CYS673 3.2 54.9 1.0 CB K:CYS697 3.2 23.9 1.0 CB K:CYS676 3.7 22.1 1.0 N K:CYS694 3.7 19.9 1.0 CG2 K:THR678 3.9 37.6 1.0 N K:CYS676 3.9 39.0 1.0 CA K:CYS694 4.0 26.6 1.0 NH2 K:ARG708 4.0 17.1 1.0 N K:CYS697 4.2 19.3 1.0 CA K:CYS697 4.3 29.0 1.0 O C:HOH2218 4.3 17.6 1.0 CA K:CYS676 4.3 36.2 1.0 CA K:CYS673 4.6 55.0 1.0 C K:CYS694 4.7 28.6 1.0 O K:CYS694 4.8 25.9 1.0 CB K:ASN675 4.8 37.0 1.0 C K:LEU693 4.9 21.5 1.0 N K:PHE677 4.9 35.8 1.0 C K:CYS676 4.9 36.9 1.0 CB K:THR678 5.0 47.5 1.0 CZ K:ARG708 5.0 33.6 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ L:Zn1713 b:31.4 occ:1.00 SG L:CYS694 2.2 41.0 1.0 SG L:CYS697 2.4 34.7 1.0 SG L:CYS676 2.4 34.0 1.0 SG L:CYS673 2.4 40.1 1.0 CB L:CYS697 3.2 18.1 1.0 CB L:CYS673 3.2 41.6 1.0 CB L:CYS694 3.4 40.1 1.0 CB L:CYS676 3.7 37.0 1.0 CG2 L:THR678 3.8 23.4 1.0 N L:CYS694 3.8 29.6 1.0 N L:CYS676 3.9 47.1 1.0 N L:CYS697 4.1 27.1 1.0 CA L:CYS694 4.2 31.9 1.0 NH2 L:ARG708 4.2 36.2 1.0 CA L:CYS697 4.2 30.4 1.0 O D:HOH2199 4.4 25.1 1.0 CA L:CYS676 4.4 41.9 1.0 CB L:ASN675 4.5 48.0 1.0 CA L:CYS673 4.7 44.0 1.0 C L:CYS694 4.8 32.9 1.0 N L:PHE677 4.9 45.2 1.0 CB L:THR678 4.9 39.3 1.0 C L:LEU693 4.9 35.1 1.0 C L:ASN675 4.9 49.6 1.0 C L:CYS676 5.0 42.0 1.0 N L:THR678 5.0 43.2 1.0 O L:CYS694 5.0 41.8 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ M:Zn1713 b:27.7 occ:1.00 SG M:CYS693 2.2 27.0 1.0 SG M:CYS675 2.2 22.7 1.0 SG M:CYS696 2.2 26.6 1.0 SG M:CYS672 2.4 32.5 1.0 CB M:CYS696 3.1 13.9 1.0 CB M:CYS672 3.3 42.5 1.0 CB M:CYS675 3.3 38.8 1.0 CB M:CYS693 3.4 27.9 1.0 N M:CYS675 3.8 36.7 1.0 N M:CYS693 3.8 33.4 1.0 CG2 M:THR677 3.9 38.0 1.0 O E:HOH2147 4.0 29.9 1.0 CA M:CYS675 4.1 38.4 1.0 NH2 M:ARG707 4.1 19.7 1.0 N M:CYS696 4.2 15.5 1.0 CA M:CYS693 4.2 23.9 1.0 CA M:CYS696 4.2 17.9 1.0 C M:CYS675 4.7 41.4 1.0 CA M:CYS672 4.8 53.8 1.0 N M:PHE676 4.8 41.7 1.0 CB M:ASN674 4.8 42.4 1.0 OD1 M:ASN674 4.8 23.4 1.0 NE M:ARG707 4.9 28.0 1.0 C M:ASN674 4.9 35.0 1.0 CB M:THR677 5.0 41.0 1.0 C M:CYS693 5.0 25.2 1.0 C M:LEU692 5.0 35.8 1.0 CZ M:ARG707 5.0 32.9 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn1713 b:31.7 occ:1.00 SG N:CYS676 2.1 33.8 1.0 SG N:CYS694 2.3 25.0 1.0 SG N:CYS697 2.4 36.6 1.0 SG N:CYS673 2.4 27.0 1.0 CB N:CYS673 3.2 40.0 1.0 CB N:CYS694 3.3 20.5 1.0 CB N:CYS676 3.4 30.8 1.0 CB N:CYS697 3.5 31.8 1.0 N N:CYS676 3.7 34.5 1.0 NH2 N:ARG708 3.9 31.2 1.0 CG2 N:THR678 3.9 27.6 1.0 N N:CYS694 4.0 30.1 1.0 O F:HOH2228 4.1 22.0 1.0 CA N:CYS676 4.1 34.1 1.0 CA N:CYS694 4.2 29.6 1.0 N N:CYS697 4.3 23.0 1.0 CA N:CYS697 4.5 24.2 1.0 CB N:ASN675 4.6 24.3 1.0 C N:CYS676 4.7 37.4 1.0 CA N:CYS673 4.7 43.2 1.0 N N:PHE677 4.8 41.4 1.0 C N:ASN675 4.9 37.7 1.0 C N:CYS694 4.9 32.3 1.0 CZ N:ARG708 4.9 27.2 1.0 NE N:ARG708 4.9 28.4 1.0 CB N:THR678 4.9 33.1 1.0 N N:THR678 4.9 46.4 1.0 O N:CYS694 5.0 44.5 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ O:Zn1712 b:33.5 occ:1.00 SG O:CYS676 2.1 29.5 1.0 SG O:CYS694 2.2 29.2 1.0 SG O:CYS697 2.3 44.2 1.0 SG O:CYS673 2.4 38.1 1.0 CB O:CYS697 3.2 34.9 1.0 CB O:CYS673 3.3 30.6 1.0 CB O:CYS694 3.4 38.6 1.0 CB O:CYS676 3.5 17.5 1.0 N O:CYS676 3.7 37.1 1.0 N O:CYS694 3.9 38.2 1.0 CG2 O:THR678 3.9 29.7 1.0 CA O:CYS676 4.1 30.4 1.0 NH2 O:ARG708 4.1 8.9 1.0 N O:CYS697 4.2 22.8 1.0 CA O:CYS694 4.2 35.3 1.0 O G:HOH2235 4.3 21.0 1.0 CA O:CYS697 4.3 34.6 1.0 CB O:ASN675 4.6 50.6 1.0 N O:PHE677 4.7 43.4 1.0 C O:CYS676 4.7 38.0 1.0 CA O:CYS673 4.7 40.3 1.0 C O:ASN675 4.8 45.3 1.0 O O:CYS694 4.8 34.2 1.0 C O:CYS694 4.8 35.8 1.0 NE O:ARG708 4.9 24.6 1.0 N O:ASN675 5.0 56.4 1.0 N O:THR678 5.0 37.9 1.0 CA O:ASN675 5.0 51.7 1.0 C O:LEU693 5.0 34.6 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of Nad-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 Nad-Bound Nmra-Area Zinc Finger Complex within 5.0Å range: probe atom residue distance (Å) B Occ P:Zn1713 b:36.6 occ:1.00 SG P:CYS676 2.0 38.0 1.0 SG P:CYS694 2.2 25.8 1.0 SG P:CYS697 2.3 37.4 1.0 SG P:CYS673 2.3 32.8 1.0 CB P:CYS697 3.2 29.3 1.0 CB P:CYS676 3.3 32.4 1.0 CB P:CYS694 3.3 35.0 1.0 CB P:CYS673 3.4 48.0 1.0 N P:CYS676 3.7 27.5 1.0 N P:CYS694 3.9 35.4 1.0 CG2 P:THR678 4.0 13.5 1.0 CA P:CYS676 4.0 40.4 1.0 CA P:CYS694 4.2 36.3 1.0 N P:CYS697 4.2 22.6 1.0 O H:HOH2196 4.2 26.0 1.0 NH2 P:ARG708 4.2 25.0 1.0 CA P:CYS697 4.3 30.9 1.0 CB P:ASN675 4.7 38.5 1.0 C P:CYS676 4.7 38.5 1.0 NE P:ARG708 4.8 37.9 1.0 N P:PHE677 4.8 41.0 1.0 CA P:CYS673 4.8 53.8 1.0 C P:ASN675 4.9 36.5 1.0 C P:CYS694 4.9 39.9 1.0 CZ P:ARG708 5.0 29.1 1.0 CB P:THR678 5.0 25.0 1.0

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