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Calcium in PDB 3lv8: 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp

Enzymatic activity of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp

All present enzymatic activity of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp:
2.7.4.9;

Protein crystallography data

The structure of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp, PDB code: 3lv8 was solved by A.S.Halavaty, G.Minasov, I.Dubrovska, J.Winsor, L.Shuvalova, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.80
Space group P 43 3 2
Cell size a, b, c (Å), α, β, γ (°) 112.973, 112.973, 112.973, 90.00, 90.00, 90.00
R / Rfree (%) 16.4 / 20.4

Other elements in 3lv8:

The structure of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp (pdb code 3lv8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp, PDB code: 3lv8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 1 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca216

b:19.2
occ:0.70
 O A:HOH480 2.1 30.6 1.0
O A:HOH482 2.3 27.5 1.0
O A:HOH314 2.3 16.0 1.0
O A:HOH479 2.3 9.4 1.0
O A:HOH481 2.4 32.5 1.0
O A:HOH441 2.4 20.6 1.0
OE2 A:GLU92 2.5 27.8 1.0
OE1 A:GLU92 2.7 23.6 1.0
CD A:GLU92 2.9 25.6 1.0
OG1 A:THR36 4.1 21.2 1.0
CG A:GLU92 4.4 21.9 1.0
NH2 A:ARG90 4.5 23.2 1.0
O A:HOH384 4.5 23.1 1.0
O A:ILE35 4.8 17.1 1.0
NE A:ARG90 4.9 24.9 1.0

Calcium binding site 2 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 2 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca217

b:29.4
occ:1.00
 O A:HOH265 2.1 17.8 0.3
O A:HOH475 2.2 18.1 1.0
O2B A:ADP213 2.4 27.6 1.0
O A:HOH478 2.4 19.0 1.0
O A:HOH477 2.4 12.2 1.0
O A:HOH476 2.5 20.9 1.0
O2B A:TYD215 2.7 21.6 0.5
PB A:ADP213 3.6 27.6 1.0
O3B A:ADP213 3.8 29.7 1.0
PB A:TYD215 3.9 24.1 0.5
O1A A:ADP213 4.0 33.5 1.0
OD2 A:ASP97 4.1 22.1 1.0
O3A A:TYD215 4.2 19.9 0.5
O3B A:TYD215 4.3 20.5 0.5
O3P A:TMP214 4.3 28.7 0.5
CB A:SER17 4.4 33.0 1.0
O A:HOH381 4.4 14.3 1.0
O A:HOH330 4.4 13.9 1.0
O A:HOH483 4.5 19.2 1.0
OD1 A:ASP97 4.5 17.4 1.0
O2A A:TYD215 4.6 17.6 0.5
O3A A:ADP213 4.6 30.4 1.0
N A:SER17 4.6 29.7 1.0
O1B A:ADP213 4.7 25.0 1.0
PA A:ADP213 4.7 31.2 1.0
CG A:ASP97 4.8 18.9 1.0
PA A:TYD215 4.8 18.7 0.5
CE A:LYS16 4.8 21.8 1.0
CA A:SER17 4.9 30.4 1.0
CB A:LYS16 4.9 23.6 1.0

Calcium binding site 3 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 3 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca218

b:24.5
occ:0.80
 OE1 A:GLU12 2.1 25.3 1.0
O1A A:TYD215 2.2 19.4 0.5
O1B A:TYD215 2.3 22.5 0.5
OE1 A:GLU158 2.4 33.1 1.0
O A:HOH434 2.4 30.7 1.0
O A:HOH327 2.5 13.7 1.0
O1P A:TMP214 2.5 27.9 0.5
CD A:GLU158 3.3 27.7 1.0
CD A:GLU12 3.4 28.3 1.0
PB A:TYD215 3.4 24.1 0.5
PA A:TYD215 3.4 18.7 0.5
P A:TMP214 3.7 28.7 0.5
CG A:GLU158 3.7 27.5 1.0
O A:HOH381 3.8 14.3 1.0
O2B A:TYD215 3.8 21.6 0.5
O3A A:TYD215 3.8 19.9 0.5
O5' A:TYD215 3.9 12.9 0.5
O2P A:TMP214 4.0 27.9 0.5
OE2 A:GLU12 4.0 26.4 1.0
O3' A:TYD215 4.1 14.3 0.5
O3' A:TMP214 4.3 20.3 0.5
C3' A:TMP214 4.3 20.6 0.5
O A:HOH265 4.3 17.8 0.3
C3' A:TYD215 4.4 12.7 0.5
OE2 A:GLU158 4.4 32.2 1.0
OD2 A:ASP155 4.4 30.8 1.0
O A:HOH230 4.4 36.7 1.0
NZ A:LYS55 4.5 37.4 1.0
CG A:GLU12 4.5 27.6 1.0
O5' A:TMP214 4.6 27.1 0.5
O3P A:TMP214 4.7 28.7 0.5
CB A:GLU12 4.7 26.8 1.0
O3B A:TYD215 4.7 20.5 0.5
O A:HOH390 4.7 23.7 1.0
O2A A:TYD215 4.8 17.6 0.5
C4' A:TYD215 4.8 13.1 0.5
C5' A:TMP214 4.8 25.3 0.5
C5' A:TYD215 4.9 13.8 0.5
C4' A:TMP214 4.9 22.4 0.5
O A:HOH483 5.0 19.2 1.0

Calcium binding site 4 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 4 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca219

b:33.1
occ:0.60
 O A:HOH232 2.0 31.3 1.0
O A:HOH231 2.3 19.0 1.0
O A:ASP179 2.4 23.4 1.0
O A:ALA176 2.5 26.0 1.0
O A:HOH392 2.6 28.1 1.0
O A:VAL182 2.7 23.7 1.0
C A:ASP179 3.3 24.7 1.0
O A:HOH293 3.6 34.5 1.0
C A:ALA176 3.7 25.1 1.0
C A:VAL182 3.8 23.4 1.0
CA A:ASP180 3.8 27.3 1.0
N A:ASP180 3.9 25.9 1.0
N A:VAL182 4.1 22.6 1.0
C A:ASP180 4.1 26.4 1.0
O A:HOH269 4.1 34.9 1.0
CB A:VAL182 4.2 21.4 1.0
CA A:VAL182 4.3 21.9 1.0
N A:ASP179 4.3 25.1 1.0
O A:ASP180 4.3 26.6 1.0
CA A:ASP179 4.4 25.1 1.0
O A:ASN177 4.5 30.3 1.0
CA A:ALA176 4.5 23.4 1.0
C A:ASN177 4.5 27.9 1.0
O A:HOH267 4.6 34.1 1.0
N A:ASN177 4.6 25.8 1.0
CA A:ASN177 4.6 28.1 1.0
N A:SER181 4.7 25.4 1.0
OD1 A:ASP180 5.0 32.0 1.0
N A:VAL183 5.0 22.8 1.0

Calcium binding site 5 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 5 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca220

b:38.1
occ:0.70
 O A:HOH267 2.3 34.1 1.0
O A:ASN177 2.4 30.3 1.0
O A:HOH268 2.5 23.4 1.0
O A:HOH293 2.6 34.5 1.0
O A:HOH291 2.7 27.0 1.0
O A:HOH292 2.7 38.2 1.0
C A:ASN177 3.6 27.9 1.0
O A:HOH232 3.8 31.3 1.0
CA A:SER178 4.2 27.1 1.0
O A:HOH243 4.3 24.0 1.0
N A:SER178 4.4 26.0 1.0
OD1 A:ASP180 4.6 32.0 1.0
CA A:ASN177 4.6 28.1 1.0
C A:SER178 4.7 26.7 1.0
O A:SER178 4.8 26.3 1.0

Calcium binding site 6 out of 6 in 3lv8

Go back to Calcium Binding Sites List in 3lv8
Calcium binding site 6 out of 6 in the 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca221

b:57.8
occ:0.70
 O A:HOH379 2.1 24.4 1.0
O A:HOH328 2.2 18.5 1.0
O A:HOH266 2.3 29.9 1.0
O A:HOH225 2.4 20.6 1.0
O A:LYS130 3.4 19.6 1.0
O A:HOH226 3.9 27.8 1.0
CE1 A:PHE129 4.2 21.0 1.0
O A:HOH401 4.3 28.3 1.0
O A:HOH359 4.3 20.6 1.0
CD1 A:PHE129 4.3 21.2 1.0
OD1 A:ASP132 4.4 22.4 1.0
OD2 A:ASP132 4.4 19.8 1.0
C A:LYS130 4.6 20.0 1.0
N A:LYS130 4.6 21.3 1.0
CG A:ASP132 4.8 21.9 1.0
O A:HOH437 4.8 28.6 1.0
CZ A:PHE129 4.9 20.7 1.0

Reference:

A.S.Halavaty, G.Minasov, I.Dubrovska, J.Winsor, L.Shuvalova, K.Kwon, W.F.Anderson, Center For Structural Genomics Of Infectious Diseases(Csgid). 1.8 Angstrom Resolution Crystal Structure of A Thymidylate Kinase (Tmk) From Vibrio Cholerae O1 Biovar Eltor Str. N16961 in Complex with Tmp, Thymidine-5'-Diphosphate and Adp To Be Published.
Page generated: Tue Jul 8 14:25:36 2025

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