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Zinc in PDB 5a8a: Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1)

Enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1)

All present enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1):
2.7.1.26;

Protein crystallography data

The structure of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1), PDB code: 5a8a was solved by B.Herguedas, M.Martinez-Julvez, J.A.Hermoso, M.Medina, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 63.81 / 1.80
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 73.590, 73.590, 149.690, 90.00, 90.00, 120.00
R / Rfree (%) 17.256 / 20.27

Other elements in 5a8a:

The structure of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1) also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1) (pdb code 5a8a). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1), PDB code: 5a8a:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5a8a

Go back to Zinc Binding Sites List in 5a8a
Zinc binding site 1 out of 2 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1)


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 the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:16.8
occ:0.80
O A:HOH2004 1.8 27.1 1.0
NE2 A:HIS325 2.0 26.0 1.0
OD1 A:ASP321 2.0 17.4 1.0
NE2 A:HIS186 2.1 21.7 1.0
CG A:ASP321 2.9 16.7 1.0
CE1 A:HIS325 2.9 28.0 1.0
CE1 A:HIS186 3.0 21.8 1.0
CD2 A:HIS325 3.0 26.5 1.0
OD2 A:ASP321 3.0 16.2 1.0
CD2 A:HIS186 3.1 21.9 1.0
O A:HOH2166 4.0 19.7 1.0
ND1 A:HIS325 4.0 28.5 1.0
CG A:HIS325 4.1 27.4 1.0
ND1 A:HIS186 4.1 21.5 1.0
CG1 A:VAL288 4.2 15.3 1.0
CG A:HIS186 4.2 22.0 1.0
CB A:ASP321 4.3 16.6 1.0
CA A:ASP321 4.9 17.9 1.0
O A:ASP321 4.9 19.2 1.0
CG2 A:VAL288 4.9 14.6 1.0

Zinc binding site 2 out of 2 in 5a8a

Go back to Zinc Binding Sites List in 5a8a
Zinc binding site 2 out of 2 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1)


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 the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Fmn and Adp (P 32 2 1) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:20.9
occ:0.75
O B:HOH2001 1.7 23.3 1.0
NE2 B:HIS325 2.0 31.2 1.0
OD1 B:ASP321 2.0 20.2 1.0
NE2 B:HIS186 2.0 23.1 1.0
CG B:ASP321 2.9 20.5 1.0
CD2 B:HIS325 2.9 31.6 1.0
CE1 B:HIS186 3.0 23.8 1.0
CE1 B:HIS325 3.0 32.5 1.0
CD2 B:HIS186 3.1 23.0 1.0
OD2 B:ASP321 3.1 19.3 1.0
O B:HOH2136 4.0 33.1 1.0
CG B:HIS325 4.1 31.9 1.0
ND1 B:HIS325 4.1 32.4 1.0
ND1 B:HIS186 4.1 23.4 1.0
CG B:HIS186 4.2 22.9 1.0
CB B:ASP321 4.3 20.7 1.0
CG1 B:VAL288 4.4 18.0 1.0
CA B:ASP321 4.8 21.6 1.0
O B:ASP321 4.8 22.8 1.0
CG2 B:VAL288 4.9 18.3 1.0

Reference:

B.Herguedas, I.Lans, M.Sebastian, J.A.Hermoso, M.Martinez-Julvez, M.Medina. Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms. Acta Crystallogr.,Sect.D V. 71 2526 2015.
ISSN: ISSN 0907-4449
PubMed: 26627660
DOI: 10.1107/S1399004715019641
Page generated: Sun Oct 27 12:43:07 2024

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