Calcium in PDB 5z8y: Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA

Protein crystallography data

The structure of Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA, PDB code: 5z8y was solved by A.Yamagata, S.Fukai, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.82 / 3.40
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 99.184, 99.858, 109.633, 91.30, 91.20, 116.47
R / Rfree (%) 20.9 / 24.1

Other elements in 5z8y:

The structure of Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA also contains other interesting chemical elements:

Zinc (Zn) 2 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA (pdb code 5z8y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA, PDB code: 5z8y:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 5z8y

Go back to Calcium Binding Sites List in 5z8y
Calcium binding site 1 out of 4 in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA


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 Human LRRTM2 in Complex with Neurexin 1BETA within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca301

b:63.3
occ:1.00
OD1 B:ASP141 2.4 91.9 1.0
OD2 B:ASP141 2.4 68.4 1.0
OD1 B:ASN212 2.4 80.5 1.0
O B:HOH401 2.4 57.8 1.0
O B:ILE210 2.4 90.0 1.0
O B:VAL158 2.4 0.8 1.0
CG B:ASP141 2.5 76.1 1.0
CB B:ASN212 2.5 63.3 1.0
CG B:ASN212 2.8 66.8 1.0
N B:ASN212 3.2 63.8 1.0
CA B:ASN212 3.5 61.6 1.0
C B:ILE210 3.6 71.1 1.0
C B:VAL158 3.6 0.1 1.0
CB B:ASP141 3.9 70.2 1.0
C B:PHE211 3.9 63.0 1.0
CA B:PHE211 4.0 67.6 1.0
OE2 A:GLU348 4.1 85.9 1.0
O A:HIS344 4.1 80.0 1.0
ND2 B:ASN212 4.1 65.3 1.0
N B:PHE211 4.2 69.6 1.0
CA B:VAL158 4.6 92.8 1.0
N B:GLY159 4.6 99.3 1.0
CG2 B:ILE210 4.6 55.4 1.0
CA B:GLY159 4.7 93.8 1.0
C B:ASN212 4.7 65.4 1.0
CA B:ILE210 4.8 67.6 1.0
O B:PHE211 4.9 71.0 1.0
CB B:ILE210 4.9 55.4 1.0
C A:HIS344 5.0 76.3 1.0
O B:ASN212 5.0 84.7 1.0

Calcium binding site 2 out of 4 in 5z8y

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Calcium binding site 2 out of 4 in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA


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 Human LRRTM2 in Complex with Neurexin 1BETA within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca301

b:63.9
occ:1.00
OD1 D:ASP141 2.4 96.7 1.0
OD2 D:ASP141 2.4 83.2 1.0
OD1 D:ASN212 2.4 79.9 1.0
O C:HOH501 2.4 58.3 1.0
O D:ILE210 2.4 89.9 1.0
O D:VAL158 2.4 0.9 1.0
CB D:ASN212 2.5 60.4 1.0
CG D:ASP141 2.5 85.5 1.0
CG D:ASN212 2.8 64.7 1.0
N D:ASN212 3.2 69.5 1.0
CA D:ASN212 3.5 63.8 1.0
C D:ILE210 3.6 76.9 1.0
C D:VAL158 3.6 0.1 1.0
CB D:ASP141 3.9 77.3 1.0
C D:PHE211 3.9 69.2 1.0
CA D:PHE211 4.0 69.3 1.0
ND2 D:ASN212 4.1 63.0 1.0
OE2 C:GLU348 4.1 94.6 1.0
O C:HIS344 4.2 76.3 1.0
N D:PHE211 4.2 73.1 1.0
CA D:VAL158 4.6 96.6 1.0
N D:GLY159 4.6 0.4 1.0
CG2 D:ILE210 4.6 55.7 1.0
CA D:GLY159 4.7 0.6 1.0
C D:ASN212 4.8 67.1 1.0
CA D:ILE210 4.8 72.7 1.0
CB D:ILE210 4.9 68.0 1.0
O D:PHE211 4.9 77.0 1.0
O D:ASN212 5.0 79.1 1.0

Calcium binding site 3 out of 4 in 5z8y

Go back to Calcium Binding Sites List in 5z8y
Calcium binding site 3 out of 4 in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA


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 Human LRRTM2 in Complex with Neurexin 1BETA within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca301

b:85.3
occ:1.00
OD1 F:ASP141 2.4 0.1 1.0
OD2 F:ASP141 2.4 0.5 1.0
OD1 F:ASN212 2.4 0.7 1.0
O F:HOH401 2.4 61.9 1.0
O F:ILE210 2.4 88.3 1.0
O F:VAL158 2.4 88.4 1.0
CB F:ASN212 2.5 97.0 1.0
CG F:ASP141 2.6 0.3 1.0
CG F:ASN212 2.8 0.5 1.0
N F:ASN212 3.1 85.2 1.0
CA F:ASN212 3.4 89.1 1.0
C F:ILE210 3.6 80.3 1.0
C F:VAL158 3.6 94.2 1.0
CB F:ASP141 3.9 0.1 1.0
C F:PHE211 3.9 81.9 1.0
CA F:PHE211 4.0 84.2 1.0
O E:HIS344 4.0 0.6 1.0
ND2 F:ASN212 4.1 0.5 1.0
OE2 E:GLU348 4.1 98.1 1.0
N F:PHE211 4.2 79.8 1.0
CA F:VAL158 4.5 96.2 1.0
N F:GLY159 4.6 97.2 1.0
CG2 F:ILE210 4.6 65.5 1.0
CA F:GLY159 4.7 0.2 1.0
C F:ASN212 4.7 93.8 1.0
CA F:ILE210 4.8 80.1 1.0
O F:PHE211 4.9 84.0 1.0
CB F:ILE210 4.9 74.7 1.0
O F:ASN212 4.9 93.4 1.0
C E:HIS344 4.9 0.3 1.0

Calcium binding site 4 out of 4 in 5z8y

Go back to Calcium Binding Sites List in 5z8y
Calcium binding site 4 out of 4 in the Crystal Structure of Human LRRTM2 in Complex with Neurexin 1BETA


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 Human LRRTM2 in Complex with Neurexin 1BETA within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca301

b:80.7
occ:1.00
OD1 H:ASP141 2.4 0.2 1.0
OD2 H:ASP141 2.4 0.8 1.0
OD1 H:ASN212 2.4 0.3 1.0
O H:HOH401 2.4 61.3 1.0
O H:ILE210 2.4 85.0 1.0
O H:VAL158 2.4 90.9 1.0
CB H:ASN212 2.5 99.0 1.0
CG H:ASP141 2.5 0.8 1.0
CG H:ASN212 2.8 0.9 1.0
N H:ASN212 3.1 89.7 1.0
CA H:ASN212 3.4 90.2 1.0
C H:ILE210 3.5 78.5 1.0
C H:VAL158 3.6 96.8 1.0
CB H:ASP141 3.9 0.4 1.0
C H:PHE211 3.9 85.8 1.0
CA H:PHE211 4.0 81.8 1.0
ND2 H:ASN212 4.1 0.1 1.0
O G:HIS344 4.1 0.1 1.0
N H:PHE211 4.2 77.4 1.0
OE2 G:GLU348 4.2 98.8 1.0
CA H:VAL158 4.5 92.5 1.0
N H:GLY159 4.6 1.0 1.0
CG2 H:ILE210 4.6 58.6 1.0
CA H:GLY159 4.7 1.0 1.0
C H:ASN212 4.7 89.7 1.0
CA H:ILE210 4.7 76.9 1.0
O H:PHE211 4.9 91.4 1.0
CB H:ILE210 4.9 73.7 1.0
O H:ASN212 5.0 85.5 1.0

Reference:

A.Yamagata, S.Goto-Ito, Y.Sato, T.Shiroshima, A.Maeda, M.Watanabe, T.Saitoh, K.Maenaka, T.Terada, T.Yoshida, T.Uemura, S.Fukai. Structural Insights Into Modulation and Selectivity of Transsynaptic Neurexin-Lrrtm Interaction. Nat Commun V. 9 3964 2018.
ISSN: ESSN 2041-1723
PubMed: 30262834
DOI: 10.1038/S41467-018-06333-8
Page generated: Sat Dec 12 05:55:40 2020

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