Zinc in PDB 2gx8: The Crystal Structure of Bacillus Cereus Protein Related to NIF3

The structure of The Crystal Structure of Bacillus Cereus Protein Related to NIF3, PDB code: 2gx8 was solved by G.Minasov, J.S.Brunzelle, L.Shuvalova, I.I.Vorontsov, F.R.Collart, A.Joachimiak, W.F.Anderson, Midwest Center For Structural Genomics(Mcsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.96 / 2.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	95.036, 95.036, 260.732, 90.00, 90.00, 120.00
R / Rfree (%)	19.6 / 26.1

The binding sites of Zinc atom in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3 (pdb code 2gx8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3, PDB code: 2gx8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn374 b:70.3 occ:1.00 NE2 A:HIS69 2.2 57.9 1.0 NE2 A:HIS333 2.4 56.9 1.0 OE2 A:GLU336 2.7 59.5 1.0 O A:HOH559 2.9 63.4 1.0 O A:HOH435 3.0 56.1 1.0 CD2 A:HIS69 3.1 59.2 1.0 CE1 A:HIS333 3.2 53.4 1.0 CE1 A:HIS69 3.2 57.9 1.0 ZN A:ZN375 3.2 67.3 1.0 CD A:GLU336 3.4 60.6 1.0 OE1 A:GLU336 3.4 64.3 1.0 CD2 A:HIS333 3.4 56.8 1.0 O A:HOH497 3.5 78.4 1.0 NE2 A:HIS103 3.7 66.5 1.0 NE2 A:HIS68 4.0 49.8 1.0 CA A:GLY291 4.1 62.4 1.0 CD2 A:HIS68 4.1 52.9 1.0 CG A:HIS69 4.3 55.3 1.0 ND1 A:HIS69 4.3 53.6 1.0 ND1 A:HIS333 4.3 54.2 1.0 CD2 A:HIS103 4.5 63.2 1.0 CG A:HIS333 4.5 57.2 1.0 O A:HOH558 4.7 74.4 1.0 CE1 A:HIS103 4.7 65.5 1.0 CG A:GLU336 4.7 55.0 1.0 N A:GLY291 4.9 62.9 1.0

Zinc binding site 2 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn375 b:67.3 occ:1.00 NE2 A:HIS68 2.1 49.8 1.0 OD1 A:ASP107 2.3 47.6 1.0 OE1 A:GLU336 2.3 64.3 1.0 O A:HOH435 2.4 56.1 1.0 OD2 A:ASP107 2.8 50.4 1.0 CG A:ASP107 2.9 50.1 1.0 CE1 A:HIS68 3.0 52.2 1.0 CD A:GLU336 3.0 60.6 1.0 OE2 A:GLU336 3.1 59.5 1.0 CD2 A:HIS68 3.1 52.9 1.0 ZN A:ZN374 3.2 70.3 1.0 O A:HOH558 3.9 74.4 1.0 NE2 A:HIS103 4.0 66.5 1.0 O A:HOH419 4.1 55.2 1.0 ND1 A:HIS68 4.1 48.5 1.0 CD2 A:HIS103 4.2 63.2 1.0 CG A:HIS68 4.2 52.3 1.0 CB A:ASP107 4.4 49.5 1.0 CG A:GLU336 4.4 55.0 1.0 CG2 A:VAL113 4.5 45.0 1.0 O A:GLY290 4.6 62.9 1.0 NE2 A:HIS69 4.7 57.9 1.0 O A:HOH526 4.7 57.5 1.0 O A:HOH497 4.8 78.4 1.0 C A:GLY290 4.9 61.6 1.0 CA A:GLY291 4.9 62.4 1.0

Zinc binding site 3 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn374 b:53.6 occ:1.00 NE2 B:HIS333 2.1 55.8 1.0 NE2 B:HIS69 2.2 56.7 1.0 OE2 B:GLU336 2.3 70.1 1.0 O B:HOH494 2.5 58.1 1.0 CD2 B:HIS69 3.0 54.0 1.0 CE1 B:HIS333 3.0 53.4 1.0 CD B:GLU336 3.1 64.6 1.0 CD2 B:HIS333 3.2 57.4 1.0 CE1 B:HIS69 3.3 55.1 1.0 OE1 B:GLU336 3.3 63.5 1.0 O B:HOH428 3.3 49.1 1.0 ZN B:ZN375 3.4 54.9 1.0 NE2 B:HIS103 4.0 69.3 1.0 CA B:GLY291 4.1 60.5 1.0 NE2 B:HIS68 4.2 52.2 1.0 CD2 B:HIS68 4.2 49.9 1.0 ND1 B:HIS333 4.2 52.8 1.0 CG B:HIS69 4.2 54.4 1.0 ND1 B:HIS69 4.3 56.8 1.0 CG B:HIS333 4.3 52.5 1.0 CG B:GLU336 4.5 54.9 1.0 CD2 B:HIS103 4.5 63.3 1.0 N B:GLY291 4.9 59.9 1.0

Zinc binding site 4 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn375 b:54.9 occ:1.00 OE1 B:GLU336 2.0 63.5 1.0 NE2 B:HIS68 2.2 52.2 1.0 OD1 B:ASP107 2.3 61.1 1.0 OD2 B:ASP107 2.7 61.0 1.0 CG B:ASP107 2.8 57.5 1.0 CD B:GLU336 2.9 64.6 1.0 CE1 B:HIS68 3.0 53.4 1.0 CD2 B:HIS68 3.3 49.9 1.0 OE2 B:GLU336 3.3 70.1 1.0 ZN B:ZN374 3.4 53.6 1.0 O B:HOH428 3.5 49.1 1.0 O B:HOH380 3.9 34.0 1.0 ND1 B:HIS68 4.2 53.6 1.0 CG B:GLU336 4.2 54.9 1.0 CD2 B:HIS103 4.2 63.3 1.0 CB B:ASP107 4.3 52.6 1.0 O B:GLY290 4.3 60.8 1.0 NE2 B:HIS103 4.3 69.3 1.0 CG B:HIS68 4.3 52.4 1.0 CG2 B:VAL113 4.6 49.0 1.0 NE2 B:HIS69 4.8 56.7 1.0 O B:HIS103 4.8 58.1 1.0 C B:GLY290 4.8 59.6 1.0 O B:HOH494 4.9 58.1 1.0 CB B:GLU336 5.0 58.8 1.0

Zinc binding site 5 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn374 b:55.7 occ:1.00 NE2 C:HIS333 2.1 65.0 1.0 NE2 C:HIS69 2.3 59.4 1.0 OE1 C:GLU336 2.5 57.7 1.0 O C:HOH418 2.6 47.9 1.0 CD2 C:HIS69 3.0 53.9 1.0 CE1 C:HIS333 3.1 61.3 1.0 CD2 C:HIS333 3.2 60.8 1.0 ZN C:ZN375 3.3 60.8 1.0 CD C:GLU336 3.3 61.1 1.0 CE1 C:HIS69 3.4 57.7 1.0 O C:HOH387 3.4 57.9 1.0 OE2 C:GLU336 3.5 63.3 1.0 NE2 C:HIS103 3.9 71.1 1.0 CA C:GLY291 4.1 56.9 1.0 CG C:HIS69 4.2 53.9 1.0 ND1 C:HIS333 4.2 62.4 1.0 CG C:HIS333 4.3 59.1 1.0 ND1 C:HIS69 4.3 55.3 1.0 NE2 C:HIS68 4.3 52.4 1.0 CD2 C:HIS68 4.3 52.4 1.0 CD2 C:HIS103 4.6 63.9 1.0 O C:HOH442 4.6 64.4 1.0 CG C:GLU336 4.7 58.6 1.0 CE1 C:HIS103 5.0 68.8 1.0 N C:GLY291 5.0 56.3 1.0

Zinc binding site 6 out of 6 in the The Crystal Structure of Bacillus Cereus Protein Related to NIF3


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Crystal Structure of Bacillus Cereus Protein Related to NIF3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn375 b:60.8 occ:1.00 OE2 C:GLU336 2.2 63.3 1.0 NE2 C:HIS68 2.2 52.4 1.0 OD1 C:ASP107 2.3 62.5 1.0 OD2 C:ASP107 2.8 59.4 1.0 CG C:ASP107 2.9 59.7 1.0 CD C:GLU336 3.0 61.1 1.0 CE1 C:HIS68 3.1 49.6 1.0 OE1 C:GLU336 3.3 57.7 1.0 CD2 C:HIS68 3.3 52.4 1.0 ZN C:ZN374 3.3 55.7 1.0 O C:HOH442 3.7 64.4 1.0 O C:HOH408 4.0 53.7 1.0 NE2 C:HIS103 4.1 71.1 1.0 CD2 C:HIS103 4.1 63.9 1.0 ND1 C:HIS68 4.2 56.4 1.0 CG C:GLU336 4.3 58.6 1.0 CG C:HIS68 4.3 54.2 1.0 CB C:ASP107 4.4 57.0 1.0 O C:GLY290 4.4 59.1 1.0 O C:HOH387 4.4 57.9 1.0 CG2 C:VAL113 4.6 56.5 1.0 NE2 C:HIS69 4.6 59.4 1.0 O C:HOH418 4.8 47.9 1.0 CG1 C:VAL113 4.9 55.2 1.0 CD2 C:HIS69 4.9 53.9 1.0 C C:GLY290 4.9 57.1 1.0 CA C:GLY291 5.0 56.9 1.0

M.H.Godsey, G.Minasov, L.Shuvalova, J.S.Brunzelle, I.I.Vorontsov, F.R.Collart, W.F.Anderson. The 2.2 A Resolution Crystal Structure of Bacillus Cereus NIF3-Family Protein Yqfo Reveals A Conserved Dimetal-Binding Motif and A Regulatory Domain Protein Sci. V. 16 1285 2007.
ISSN: ISSN 0961-8368
PubMed: 17586767
DOI: 10.1110/PS.062674007