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Magnesium 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:

Zinc (Zn) 2 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium 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 Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 5a8a

Go back to Magnesium Binding Sites List in 5a8a
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502

b:10.8
occ:1.00
 O1P A:FMN401 2.0 15.3 1.0
O1A A:ADP501 2.1 15.3 1.0
O3B A:ADP501 2.1 15.2 1.0
O A:THR208 2.1 12.7 1.0
OD1 A:ASN210 2.1 14.4 1.0
OG1 A:THR208 2.2 13.0 1.0
C A:THR208 3.1 12.4 1.0
CG A:ASN210 3.1 15.0 1.0
PB A:ADP501 3.2 16.4 1.0
CB A:THR208 3.3 12.3 1.0
PA A:ADP501 3.3 15.8 1.0
P A:FMN401 3.4 15.5 1.0
CA A:THR208 3.5 12.5 1.0
N A:THR208 3.5 13.4 1.0
O3A A:ADP501 3.6 15.4 1.0
ND2 A:ASN210 3.6 15.5 1.0
O1B A:ADP501 3.6 16.2 1.0
O3P A:FMN401 3.8 16.3 1.0
O A:HOH2010 3.9 11.9 1.0
C5' A:ADP501 3.9 14.6 1.0
OE1 A:GLU268 4.0 15.7 1.0
O5' A:ADP501 4.1 15.3 1.0
O2P A:FMN401 4.2 15.6 1.0
N A:ALA209 4.2 11.9 1.0
CB A:ASN210 4.4 14.4 1.0
N A:ASN210 4.4 13.4 1.0
O2B A:ADP501 4.5 16.8 1.0
O5' A:FMN401 4.5 16.1 1.0
CG2 A:THR208 4.5 12.5 1.0
O2A A:ADP501 4.5 16.1 1.0
CD A:GLU268 4.6 15.1 1.0
C5' A:FMN401 4.6 15.6 1.0
C A:ALA209 4.7 12.6 1.0
CA A:ALA209 4.7 12.3 1.0
C A:PRO207 4.8 13.9 1.0
CA A:ASN210 4.9 13.6 1.0
CG A:GLU268 4.9 14.2 1.0

Magnesium binding site 2 out of 2 in 5a8a

Go back to Magnesium Binding Sites List in 5a8a
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg502

b:7.7
occ:1.00
 O1P B:FMN401 1.9 11.7 1.0
O3B B:ADP501 2.0 12.8 1.0
ND2 B:ASN210 2.1 11.9 1.0
O1A B:ADP501 2.1 12.8 1.0
O B:THR208 2.2 11.5 1.0
OG1 B:THR208 2.2 11.8 1.0
C B:THR208 3.1 11.8 1.0
PB B:ADP501 3.1 13.8 1.0
CG B:ASN210 3.2 12.6 1.0
CB B:THR208 3.3 11.8 1.0
P B:FMN401 3.4 12.9 1.0
PA B:ADP501 3.4 13.3 1.0
CA B:THR208 3.5 11.7 1.0
OD1 B:ASN210 3.6 13.9 1.0
O1B B:ADP501 3.6 13.3 1.0
N B:THR208 3.6 12.0 1.0
O3A B:ADP501 3.6 13.8 1.0
O3P B:FMN401 3.8 13.2 1.0
OE1 B:GLU268 3.9 13.6 1.0
O B:HOH2007 4.0 13.7 1.0
C5' B:ADP501 4.0 13.7 1.0
O2P B:FMN401 4.2 12.9 1.0
O5' B:ADP501 4.2 13.2 1.0
N B:ALA209 4.3 12.1 1.0
CB B:ASN210 4.4 12.6 1.0
N B:ASN210 4.4 12.4 1.0
O5' B:FMN401 4.4 12.6 1.0
O2B B:ADP501 4.5 13.6 1.0
CD B:GLU268 4.5 13.4 1.0
CG2 B:THR208 4.6 11.6 1.0
O2A B:ADP501 4.6 13.0 1.0
C5' B:FMN401 4.6 12.2 1.0
C B:ALA209 4.7 12.3 1.0
CA B:ALA209 4.8 12.2 1.0
CA B:ASN210 4.8 12.6 1.0
C B:PRO207 4.9 12.7 1.0
CG B:GLU268 4.9 13.2 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 Sep 29 00:20:23 2024

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