Calcium in PDB 2rex: Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase

Protein crystallography data

The structure of Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase, PDB code: 2rex was solved by Y.Tong, W.Tempel, L.Shen, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park, Structural Genomics Consortium (Sgc), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.136, 71.653, 101.885, 90.00, 128.36, 90.00
R / Rfree (%) 21.5 / 24.8

Other elements in 2rex:

The structure of Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase (pdb code 2rex). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase, PDB code: 2rex:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 2rex

Go back to Calcium Binding Sites List in 2rex
Calcium binding site 1 out of 2 in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase


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 Effector Domain of PLXNB1 Bound with RND1 Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca551

b:30.9
occ:1.00
O B:HOH566 2.2 28.5 1.0
O B:TYR38 2.3 34.8 1.0
OE1 B:GLU40 2.4 29.6 1.0
O B:HOH564 2.5 22.5 1.0
O B:HOH565 2.5 23.0 1.0
CD B:GLU40 3.4 29.8 1.0
C B:TYR38 3.5 34.6 1.0
OE2 B:GLU40 3.8 28.5 1.0
N B:TYR38 4.3 36.0 1.0
CA B:TYR38 4.3 35.3 1.0
CB B:TYR38 4.4 34.7 1.0
N B:GLU40 4.5 33.8 1.0
N B:PRO39 4.5 34.5 1.0
CD2 B:TYR38 4.6 33.7 1.0
CA B:PRO39 4.6 34.7 1.0
CG B:GLU40 4.8 31.6 1.0
SG B:CYS37 4.8 43.7 1.0
CG B:TYR38 5.0 34.4 1.0
CB B:GLU40 5.0 33.0 1.0

Calcium binding site 2 out of 2 in 2rex

Go back to Calcium Binding Sites List in 2rex
Calcium binding site 2 out of 2 in the Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase


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 Effector Domain of PLXNB1 Bound with RND1 Gtpase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca551

b:32.6
occ:1.00
O D:HOH583 2.2 27.6 1.0
OE1 D:GLU40 2.3 31.3 1.0
O D:TYR38 2.3 34.5 1.0
O D:HOH584 2.5 22.7 1.0
O D:HOH582 2.6 26.5 1.0
CD D:GLU40 3.3 32.4 1.0
C D:TYR38 3.5 34.6 1.0
OE2 D:GLU40 3.7 31.7 1.0
N D:TYR38 4.2 36.5 1.0
CA D:TYR38 4.3 34.8 1.0
CB D:TYR38 4.4 34.2 1.0
N D:GLU40 4.6 33.2 1.0
O D:HOH589 4.6 40.7 1.0
N D:PRO39 4.6 34.0 1.0
CD2 D:TYR38 4.6 32.5 1.0
SG D:CYS37 4.7 43.0 1.0
CG D:GLU40 4.7 31.3 1.0
CA D:PRO39 4.8 34.0 1.0
CB D:GLU40 4.9 31.9 1.0

Reference:

Y.Tong, W.Tempel, L.Shen, C.H.Arrowsmith, A.M.Edwards, M.Sundstrom, J.Weigelt, A.Bochkarev, H.Park. Crystal Structure of the Effector Domain of PLXNB1 Bound with RND1 Gtpase. To Be Published.
Page generated: Sat Dec 12 03:52:08 2020

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