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Calcium in PDB 1t9h: The Crystal Structure of Yloq, A Circularly Permuted Gtpase.

Protein crystallography data

The structure of The Crystal Structure of Yloq, A Circularly Permuted Gtpase., PDB code: 1t9h was solved by V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Cladiere, A.A.Antson, M.N.Isupov, S.J.Seror, A.J.Wilkinson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.50 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 47.970, 47.970, 279.890, 90.00, 90.00, 90.00
R / Rfree (%) 14.4 / 17.8

Other elements in 1t9h:

The structure of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Uranium (U) 8 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase. (pdb code 1t9h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase., PDB code: 1t9h:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 1t9h

Go back to Calcium Binding Sites List in 1t9h
Calcium binding site 1 out of 4 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca412

b:21.5
occ:1.00
O A:HOH549 2.3 38.6 1.0
OH A:TYR145 2.5 21.4 1.0
OD1 A:ASP143 2.9 32.9 1.0
CG A:ASP143 3.4 26.4 1.0
O A:HOH597 3.4 44.4 1.0
CZ A:TYR145 3.5 19.2 1.0
OD2 A:ASP143 3.8 33.2 1.0
CE2 A:TYR145 3.9 21.5 1.0
NE2 A:HIS161 4.2 24.4 1.0
CB A:ASP143 4.2 20.4 1.0
O A:HOH443 4.5 21.9 1.0
CE1 A:HIS161 4.5 24.1 1.0
CE1 A:TYR145 4.6 20.6 1.0

Calcium binding site 2 out of 4 in 1t9h

Go back to Calcium Binding Sites List in 1t9h
Calcium binding site 2 out of 4 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca413

b:27.2
occ:1.00
OE2 A:GLU247 3.1 40.5 1.0
O A:HOH602 3.4 42.8 1.0
OE1 A:GLU247 3.8 38.3 1.0
CD A:GLU247 3.8 35.7 1.0
NE A:ARG246 4.6 21.1 1.0
CG A:ARG246 4.9 18.2 1.0
CD A:ARG246 4.9 21.4 1.0

Calcium binding site 3 out of 4 in 1t9h

Go back to Calcium Binding Sites List in 1t9h
Calcium binding site 3 out of 4 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca414

b:44.8
occ:1.00
O A:HOH658 2.2 45.2 0.3
O A:HOH663 2.3 47.3 0.3
OE1 A:GLU210 2.7 30.6 1.0
OE2 A:GLU210 2.7 29.5 1.0
CD A:GLU210 3.0 26.8 1.0
O A:HOH693 3.3 52.5 1.0
O A:HOH708 3.4 60.0 1.0
O A:HOH473 3.8 28.8 1.0
NZ A:LYS8 4.1 37.0 1.0
O A:HOH493 4.3 31.1 1.0
CG A:GLU210 4.6 22.7 1.0
O A:HOH669 4.6 50.3 1.0
CD A:LYS8 4.7 28.1 1.0

Calcium binding site 4 out of 4 in 1t9h

Go back to Calcium Binding Sites List in 1t9h
Calcium binding site 4 out of 4 in the The Crystal Structure of Yloq, A Circularly Permuted Gtpase.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Crystal Structure of Yloq, A Circularly Permuted Gtpase. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca415

b:39.6
occ:1.00
O A:HOH521 1.8 40.2 1.0
O A:HOH595 1.9 49.2 1.0
OE1 A:GLU286 2.2 43.5 1.0
CD A:GLU286 2.9 39.3 1.0
OE2 A:GLU286 3.0 43.8 1.0
O A:HOH646 3.5 53.7 1.0
O A:HOH430 3.7 19.1 1.0
O A:HOH482 3.9 30.6 1.0
O A:HOH697 4.1 54.0 1.0
CG A:GLU286 4.4 31.1 1.0
CB A:ALA95 4.4 20.8 1.0

Reference:

V.M.Levdikov, E.V.Blagova, J.A.Brannigan, L.Cladiere, A.A.Antson, M.N.Isupov, S.J.Seror, A.J.Wilkinson. The Crystal Structure of Yloq, A Circularly Permuted Gtpase Essential For Bacillus Subtilis Viability. J.Mol.Biol. V. 340 767 2004.
ISSN: ISSN 0022-2836
PubMed: 15223319
DOI: 10.1016/J.JMB.2004.05.029
Page generated: Wed Oct 28 07:26:13 2020

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