Atomistry » Calcium » PDB 3ljz-3lzk » 3lv8
Atomistry »
  Calcium »
    PDB 3ljz-3lzk »
      3lv8 »

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: Sat Jul 13 13:18:42 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy