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Calcium in PDB 5a88: Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp

Enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp

All present enzymatic activity of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp:
2.7.1.26; 2.7.7.2;

Protein crystallography data

The structure of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp, PDB code: 5a88 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) 37.82 / 2.08
Space group P 32
Cell size a, b, c (Å), α, β, γ (°) 68.664, 68.664, 147.006, 90.00, 90.00, 120.00
R / Rfree (%) 15.884 / 18.869

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp (pdb code 5a88). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp, PDB code: 5a88:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5a88

Go back to Calcium Binding Sites List in 5a88
Calcium binding site 1 out of 4 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1340

b:33.1
occ:1.00
 O2 A:GOL1338 2.3 42.7 1.0
O1A A:ADP501 2.3 31.2 1.0
O3B A:ADP501 2.4 30.4 1.0
OD1 A:ASN210 2.4 32.4 1.0
O A:THR208 2.4 28.7 1.0
OG1 A:THR208 2.4 33.8 1.0
O1 A:GOL1338 2.6 38.2 1.0
C A:THR208 3.3 30.2 1.0
C2 A:GOL1338 3.4 46.3 1.0
CG A:ASN210 3.4 30.9 1.0
PB A:ADP501 3.4 32.2 1.0
C1 A:GOL1338 3.5 41.1 1.0
CB A:THR208 3.5 34.6 1.0
PA A:ADP501 3.6 34.6 1.0
CA A:THR208 3.7 32.0 1.0
N A:THR208 3.7 33.7 1.0
O1B A:ADP501 3.7 33.1 1.0
ND2 A:ASN210 3.9 32.2 1.0
O3A A:ADP501 3.9 34.3 1.0
C5' A:ADP501 4.1 32.5 1.0
O A:HOH2009 4.3 24.4 1.0
O5' A:ADP501 4.4 33.9 1.0
C3 A:GOL1338 4.4 50.0 1.0
N A:ALA209 4.5 29.1 1.0
N A:ASN210 4.5 28.7 1.0
O A:HOH2022 4.5 51.1 1.0
CB A:ASN210 4.6 29.2 1.0
CG2 A:THR208 4.8 35.2 1.0
O2B A:ADP501 4.8 31.5 1.0
O A:HOH2017 4.8 49.0 1.0
O2A A:ADP501 4.8 35.2 1.0
OE1 A:GLU268 4.8 54.4 1.0
C A:ALA209 4.9 29.9 1.0
C A:PRO207 5.0 36.2 1.0

Calcium binding site 2 out of 4 in 5a88

Go back to Calcium Binding Sites List in 5a88
Calcium binding site 2 out of 4 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1338

b:32.9
occ:1.00
 O3B B:ADP501 2.2 31.5 1.0
O B:THR208 2.3 31.2 1.0
O1A B:ADP501 2.3 33.2 1.0
OG1 B:THR208 2.3 33.7 1.0
OD1 B:ASN210 2.4 32.4 1.0
O2 B:GOL1337 2.5 46.2 1.0
O1 B:GOL1337 2.5 46.4 1.0
C B:THR208 3.3 30.3 1.0
CG B:ASN210 3.3 32.9 1.0
PB B:ADP501 3.4 34.5 1.0
C1 B:GOL1337 3.5 47.5 1.0
C2 B:GOL1337 3.5 52.3 1.0
CB B:THR208 3.5 32.3 1.0
PA B:ADP501 3.6 36.2 1.0
CA B:THR208 3.7 32.6 1.0
N B:THR208 3.7 33.8 1.0
ND2 B:ASN210 3.7 33.0 1.0
OE2 B:GLU268 3.8 53.7 1.0
O1B B:ADP501 3.8 34.8 1.0
O3A B:ADP501 3.8 34.4 1.0
C5' B:ADP501 4.1 33.7 1.0
O B:HOH2006 4.2 28.6 1.0
O5' B:ADP501 4.4 35.1 1.0
N B:ALA209 4.5 29.0 1.0
N B:ASN210 4.6 29.9 1.0
CB B:ASN210 4.6 31.7 1.0
O B:HOH2013 4.6 52.0 1.0
C3 B:GOL1337 4.6 52.9 1.0
CD B:GLU268 4.7 47.4 1.0
O2A B:ADP501 4.7 37.0 1.0
CG2 B:THR208 4.7 35.4 1.0
CG B:GLU268 4.8 41.9 1.0
O2B B:ADP501 4.8 33.7 1.0
C B:ALA209 4.9 30.7 1.0
CA B:ALA209 5.0 29.5 1.0
C B:PRO207 5.0 37.9 1.0

Calcium binding site 3 out of 4 in 5a88

Go back to Calcium Binding Sites List in 5a88
Calcium binding site 3 out of 4 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1340

b:34.8
occ:1.00
 O3B C:ADP501 2.3 34.6 1.0
O2 C:GOL1338 2.3 50.4 1.0
OG1 C:THR208 2.3 36.7 1.0
O C:THR208 2.3 33.3 1.0
OD1 C:ASN210 2.4 32.0 1.0
O1A C:ADP501 2.4 34.2 1.0
O1 C:GOL1338 2.8 49.7 1.0
C C:THR208 3.2 33.0 1.0
CG C:ASN210 3.4 32.5 1.0
CB C:THR208 3.4 36.0 1.0
C2 C:GOL1338 3.5 52.9 1.0
PB C:ADP501 3.5 37.7 1.0
PA C:ADP501 3.6 36.8 1.0
CA C:THR208 3.6 35.4 1.0
N C:THR208 3.7 37.4 1.0
C1 C:GOL1338 3.7 48.6 1.0
O1B C:ADP501 3.8 37.0 1.0
ND2 C:ASN210 3.8 33.9 1.0
O3A C:ADP501 3.9 37.7 1.0
C5' C:ADP501 4.1 35.0 1.0
O C:HOH2010 4.2 31.3 1.0
C3 C:GOL1338 4.3 55.0 1.0
N C:ALA209 4.4 31.6 1.0
O5' C:ADP501 4.4 37.3 1.0
CB C:ASN210 4.6 31.2 1.0
N C:ASN210 4.6 31.2 1.0
CG2 C:THR208 4.6 38.3 1.0
O1 C:GOL1339 4.6 47.4 1.0
O2 C:GOL1339 4.8 47.0 1.0
O2B C:ADP501 4.8 37.8 1.0
O2A C:ADP501 4.8 37.0 1.0
C C:ALA209 4.9 30.1 1.0
C C:PRO207 5.0 38.9 1.0
CA C:ALA209 5.0 31.4 1.0
CA C:ASN210 5.0 30.4 1.0

Calcium binding site 4 out of 4 in 5a88

Go back to Calcium Binding Sites List in 5a88
Calcium binding site 4 out of 4 in the Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of the Riboflavin Kinase Module of Fad Synthetase From Corynebacterium Ammoniagenes in Complex with Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1338

b:46.3
occ:1.00
 OG1 D:THR208 2.2 45.9 1.0
O1A D:ADP501 2.3 47.6 1.0
O3B D:ADP501 2.3 48.2 1.0
O D:THR208 2.4 43.9 1.0
OD1 D:ASN210 2.4 41.2 1.0
O2 D:GOL1337 2.4 62.8 1.0
O3 D:GOL1337 2.6 62.5 1.0
CG D:ASN210 3.3 42.8 1.0
C D:THR208 3.3 44.3 1.0
C2 D:GOL1337 3.4 66.9 1.0
PB D:ADP501 3.4 48.2 1.0
CB D:THR208 3.4 46.4 1.0
C3 D:GOL1337 3.4 65.3 1.0
PA D:ADP501 3.5 49.3 1.0
ND2 D:ASN210 3.6 44.0 1.0
CA D:THR208 3.7 46.5 1.0
O1B D:ADP501 3.7 51.3 1.0
N D:THR208 3.8 48.1 1.0
O3A D:ADP501 3.8 49.4 1.0
C5' D:ADP501 4.1 47.2 1.0
O D:HOH2007 4.2 54.5 1.0
O D:HOH2005 4.2 34.8 1.0
O5' D:ADP501 4.4 48.1 1.0
N D:ASN210 4.5 40.3 1.0
N D:ALA209 4.5 43.2 1.0
CB D:ASN210 4.6 40.4 1.0
CG2 D:THR208 4.6 46.9 1.0
C1 D:GOL1337 4.7 67.6 1.0
O2A D:ADP501 4.7 49.6 1.0
O2B D:ADP501 4.8 50.1 1.0
C D:ALA209 4.9 40.6 1.0
CA D:ALA209 5.0 41.9 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 Jul 14 16:24:05 2024

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