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Calcium in PDB 5vrb: Crystal Structure of A Transketolase From Neisseria Gonorrhoeae

Enzymatic activity of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae

All present enzymatic activity of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae:
2.2.1.1;

Protein crystallography data

The structure of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae, PDB code: 5vrb was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.59 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.450, 114.210, 125.690, 90.00, 90.11, 90.00
R / Rfree (%) 15.1 / 19.1

Calcium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Calcium atom in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae (pdb code 5vrb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae, PDB code: 5vrb:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 12 in 5vrb

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Calcium binding site 1 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:22.2
occ:1.00
 O A:HOH1152 2.4 25.8 1.0
O B:HOH1000 2.4 23.2 1.0
O A:HOH1181 2.4 28.7 1.0
OE2 A:GLU633 2.4 18.6 1.0
O B:HOH1339 2.5 26.1 1.0
O A:HOH1196 2.5 29.7 1.0
OE1 A:GLU633 2.6 17.9 1.0
O B:HOH1201 2.7 29.5 1.0
CD A:GLU633 2.9 16.7 1.0
O A:HOH1164 3.7 27.4 1.0
O B:HOH823 3.9 37.1 1.0
O C:HOH1116 4.1 27.1 1.0
O B:HOH1381 4.3 32.9 1.0
O B:HOH970 4.3 13.3 1.0
OE1 B:GLU99 4.4 17.9 1.0
CG A:GLU633 4.4 13.6 1.0
O A:HOH1133 4.4 17.4 0.6
O B:HOH1052 4.5 16.1 1.0
O B:HOH1008 4.5 24.1 1.0
NH2 A:ARG630 4.6 15.4 1.0
O A:HOH1014 4.9 16.1 1.0

Calcium binding site 2 out of 12 in 5vrb

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Calcium binding site 2 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


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 A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:50.6
occ:1.00
 O A:HOH842 2.4 36.3 1.0
OD2 A:ASP152 2.4 32.3 1.0
OD1 A:ASN183 2.4 30.8 1.0
OD1 A:ASN182 2.5 28.3 1.0
O A:HOH1206 2.6 42.4 1.0
CG A:ASN183 3.4 34.8 1.0
CG A:ASP152 3.4 24.6 1.0
CG A:ASN182 3.6 30.6 1.0
ND2 A:ASN183 3.8 28.6 1.0
CB A:ASP152 3.8 21.6 1.0
ND2 A:ASN182 4.1 36.5 1.0
O A:HOH952 4.2 19.1 1.0
OD1 A:ASP152 4.5 27.0 1.0
C A:ASN182 4.6 27.0 1.0
O A:ASN182 4.7 33.4 1.0
CB A:ASN183 4.7 35.4 1.0
N A:ASN183 4.8 31.7 1.0
CB A:ASN182 4.9 22.6 1.0
CA A:ASN183 5.0 37.2 1.0
N A:ASN182 5.0 17.9 1.0

Calcium binding site 3 out of 12 in 5vrb

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Calcium binding site 3 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


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 A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:31.7
occ:1.00
 OD3 A:OCS154 2.9 37.8 1.0
N A:GLY153 3.2 13.4 1.0
C A:GLY151 3.5 16.4 1.0
CA A:GLY151 3.6 15.1 1.0
CA A:GLY153 3.6 14.8 1.0
N A:ASP152 3.7 15.8 1.0
N A:OCS154 3.7 12.7 1.0
NE2 A:HIS63 3.7 46.6 1.0
CB A:ASN61 3.9 30.9 1.0
O A:GLY151 4.0 15.4 1.0
N A:GLY151 4.0 14.4 1.0
SG A:OCS154 4.1 18.0 1.0
C A:GLY153 4.1 13.9 1.0
C A:ASP152 4.2 15.9 1.0
CD2 A:LEU113 4.4 20.6 1.0
OD1 A:OCS154 4.4 17.3 1.0
CD1 A:LEU113 4.4 23.3 1.0
CE1 A:HIS63 4.5 45.8 1.0
CA A:ASP152 4.5 15.7 1.0
ND2 A:ASN61 4.6 38.5 1.0
CB A:OCS154 4.7 13.8 1.0
CA A:OCS154 4.8 12.1 1.0
CD2 A:HIS63 4.8 43.4 1.0
O A:HOH824 4.8 33.1 1.0
O A:HOH952 4.8 19.1 1.0
CG A:ASN61 4.8 36.7 1.0
CA A:ASN61 4.9 28.0 1.0

Calcium binding site 4 out of 12 in 5vrb

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Calcium binding site 4 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


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 A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:25.4
occ:1.00
 O A:HOH1157 2.3 38.8 1.0
O B:HOH1261 2.4 33.2 1.0
OE2 B:GLU633 2.4 23.2 1.0
O A:HOH906 2.5 33.2 1.0
O B:HOH1217 2.5 37.8 1.0
O A:HOH1252 2.5 30.8 1.0
O B:HOH1271 2.5 37.2 1.0
OE1 B:GLU633 2.6 18.2 1.0
CD B:GLU633 2.8 22.0 1.0
O B:HOH1121 3.7 34.4 1.0
O A:HOH950 4.1 15.5 1.0
CG B:GLU633 4.4 21.4 1.0
OE1 A:GLU99 4.4 21.5 1.0
O A:HOH1000 4.4 34.9 1.0
O A:HOH1024 4.8 14.7 1.0

Calcium binding site 5 out of 12 in 5vrb

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Calcium binding site 5 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:22.8
occ:1.00
 O B:ILE184 2.3 21.5 1.0
OD2 B:ASP152 2.3 25.5 1.0
OD1 B:ASN182 2.4 19.1 1.0
O B:HOH998 2.4 14.1 1.0
O B:HOH1281 2.5 22.6 1.0
O B:HOH1242 2.7 18.5 1.0
CG B:ASN182 3.2 21.0 1.0
CG B:ASP152 3.4 20.6 1.0
C B:ILE184 3.5 23.9 1.0
ND2 B:ASN182 3.5 17.8 1.0
CB B:ASP152 3.7 14.8 1.0
N B:ILE184 4.0 23.1 1.0
N B:ASP152 4.1 17.1 1.0
CA B:ILE184 4.2 27.5 1.0
O B:HOH857 4.2 19.7 1.0
O B:HOH1291 4.4 24.0 1.0
O B:HOH962 4.4 30.4 1.0
O B:HOH983 4.5 40.1 1.0
O B:ASP180 4.5 17.8 1.0
OD1 B:ASP152 4.5 22.9 1.0
N B:SER185 4.5 21.0 1.0
CA B:ASP152 4.6 12.7 1.0
CB B:ASN182 4.6 15.5 1.0
CB B:ILE184 4.6 27.2 1.0
CA B:SER185 4.7 24.8 1.0
N B:ASN182 4.7 15.1 1.0
N B:ASN183 4.8 19.2 1.0
C B:ASN182 4.9 21.4 1.0
CA B:ASN182 5.0 15.8 1.0

Calcium binding site 6 out of 12 in 5vrb

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Calcium binding site 6 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca703

b:30.3
occ:1.00
 O B:HOH1281 3.1 22.6 1.0
O B:HOH962 3.1 30.4 1.0
N B:GLY153 3.3 11.6 1.0
OD3 B:OCS154 3.3 39.2 1.0
CA B:GLY153 3.7 11.3 1.0
CA B:GLY151 3.7 15.6 1.0
CE1 B:HIS63 3.7 31.8 1.0
C B:GLY151 3.8 19.6 1.0
N B:ASP152 3.8 17.1 1.0
CB B:ASN61 4.0 21.3 1.0
N B:OCS154 4.0 10.5 1.0
N B:GLY151 4.3 12.1 1.0
NE2 B:HIS63 4.3 27.1 1.0
CD1 B:LEU113 4.3 19.7 1.0
C B:ASP152 4.3 12.1 1.0
O B:GLY151 4.4 15.2 1.0
C B:GLY153 4.4 12.1 1.0
O B:HOH998 4.4 14.1 1.0
O B:HOH1291 4.4 24.0 1.0
CD2 B:LEU113 4.5 18.2 1.0
O B:HOH857 4.5 19.7 1.0
SG B:OCS154 4.5 18.6 1.0
CA B:ASP152 4.6 12.7 1.0
OD1 B:OCS154 4.7 24.5 1.0
ND1 B:HIS63 4.9 25.8 1.0
CA B:ASN61 4.9 20.6 1.0
ND2 B:ASN61 4.9 22.1 1.0

Calcium binding site 7 out of 12 in 5vrb

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Calcium binding site 7 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca703

b:19.3
occ:1.00
 OG C:SER390 2.4 19.6 1.0
O C:HOH869 2.4 19.4 1.0
O C:SER390 2.4 18.3 1.0
O1 C:EDO701 2.4 21.9 1.0
O C:HOH1098 2.5 23.8 1.0
O C:HOH1192 2.5 32.7 1.0
O C:HOH1095 2.5 23.2 1.0
O2 C:EDO701 2.6 23.6 1.0
C C:SER390 3.3 16.5 1.0
C2 C:EDO701 3.4 24.3 1.0
C1 C:EDO701 3.4 26.9 1.0
CB C:SER390 3.5 15.9 1.0
CA C:SER390 3.8 14.9 1.0
N C:SER390 4.0 14.1 1.0
O C:TRP387 4.4 19.0 1.0
O C:HOH1206 4.4 35.4 1.0
OD2 C:ASP386 4.4 21.4 1.0
N C:VAL391 4.5 16.9 1.0
OD1 C:ASP386 4.5 16.0 1.0
O C:SER388 4.8 19.2 1.0
O C:HOH1154 4.9 19.5 1.0
CG C:ASP386 4.9 20.2 1.0
CA C:VAL391 4.9 17.6 1.0
C C:ASN389 5.0 20.0 1.0

Calcium binding site 8 out of 12 in 5vrb

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Calcium binding site 8 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca704

b:32.8
occ:1.00
 O D:HOH875 2.3 30.8 1.0
O C:HOH1162 2.3 52.9 1.0
O C:HOH1199 2.4 41.1 1.0
O C:HOH1188 2.4 39.0 1.0
O D:HOH1222 2.5 37.1 1.0
O C:HOH1187 2.6 34.2 1.0
OE2 C:GLU633 2.6 20.9 1.0
OE1 C:GLU633 2.7 22.5 1.0
CD C:GLU633 3.0 20.6 1.0
O C:HOH972 3.6 26.6 1.0
O D:HOH935 4.1 14.3 1.0
O C:HOH1201 4.2 40.4 1.0
O D:HOH881 4.3 35.9 1.0
O C:HOH1258 4.3 42.5 1.0
OE1 D:GLU99 4.3 21.3 1.0
CD2 D:HIS91 4.4 24.9 1.0
CG C:GLU633 4.5 20.1 1.0
O D:HOH981 4.5 29.8 1.0
O D:HOH1246 4.7 32.0 1.0
NH2 C:ARG630 4.8 14.8 1.0
O D:HOH899 4.8 18.7 1.0

Calcium binding site 9 out of 12 in 5vrb

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Calcium binding site 9 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca705

b:47.8
occ:1.00
 OD2 C:ASP152 2.4 35.7 1.0
O C:HOH1212 2.4 43.1 1.0
OD1 C:ASN183 2.5 43.4 1.0
OD1 C:ASN182 2.5 35.5 1.0
O C:HOH893 2.5 29.7 1.0
CG C:ASN183 3.4 43.2 1.0
CG C:ASP152 3.5 31.6 1.0
CG C:ASN182 3.6 37.7 1.0
ND2 C:ASN183 3.7 37.0 1.0
CB C:ASP152 4.0 20.1 1.0
ND2 C:ASN182 4.2 40.1 1.0
O C:ASN182 4.4 42.1 1.0
O C:HOH860 4.5 18.9 1.0
C C:ASN182 4.5 39.8 1.0
OD1 C:ASP152 4.5 35.1 1.0
CB C:ASN183 4.7 42.9 1.0
N C:ASN183 4.8 42.9 1.0
CB C:ASN182 4.8 31.3 1.0
N C:ASN182 5.0 20.7 1.0

Calcium binding site 10 out of 12 in 5vrb

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Calcium binding site 10 out of 12 in the Crystal Structure of A Transketolase From Neisseria Gonorrhoeae


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Transketolase From Neisseria Gonorrhoeae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca704

b:39.5
occ:1.00
 OD2 D:ASP152 2.3 33.8 1.0
OD1 D:ASN182 2.4 30.7 1.0
O D:HOH924 2.4 17.8 1.0
CG D:ASN182 3.2 33.2 1.0
O D:HOH1158 3.2 38.2 1.0
CG D:ASP152 3.3 30.7 1.0
ND2 D:ASN182 3.4 32.9 1.0
CB D:ASP152 3.7 22.3 1.0
N D:ASP152 4.2 11.9 1.0
O D:HOH825 4.4 30.6 1.0
OD1 D:ASP152 4.4 30.2 1.0
O D:ASP180 4.5 20.7 1.0
O D:HOH872 4.5 32.6 1.0
CA D:ASP152 4.6 15.6 1.0
CB D:ASN182 4.6 21.9 1.0
N D:ASN182 4.8 18.4 1.0

Reference:

T.E.Edwards, S.L.Delker, D.D.Lorimer, Seattle Structural Genomics Center For Infectious Disease(Ssgcid). Crystal Structure of A Transketolase From Neisseria Gonorrhoeae To Be Published.
Page generated: Wed Jul 9 10:51:25 2025

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