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Calcium in PDB 4neh: An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2

Protein crystallography data

The structure of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2, PDB code: 4neh was solved by M.Sen, K.Yuki, T.A.Springer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.66 / 2.75
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 126.967, 131.444, 190.477, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 22.5

Other elements in 4neh:

The structure of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 (pdb code 4neh). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2, PDB code: 4neh:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4neh

Go back to Calcium Binding Sites List in 4neh
Calcium binding site 1 out of 5 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1101

b:46.5
occ:1.00
 OD1 A:ASP582 2.3 42.0 1.0
OD1 A:ASP578 2.3 61.2 1.0
O A:LEU580 2.3 57.1 1.0
OG1 A:THR576 2.4 53.2 1.0
OD1 A:ASP574 2.4 54.1 1.0
O A:HOH1204 2.4 31.7 1.0
OD2 A:ASP582 2.4 38.5 1.0
CG A:ASP582 2.7 46.3 1.0
CG A:ASP578 3.0 63.3 1.0
OD2 A:ASP578 3.0 65.2 1.0
C A:LEU580 3.4 45.2 1.0
CG A:ASP574 3.4 53.5 1.0
CB A:THR576 3.6 55.5 1.0
N A:THR576 3.9 39.7 1.0
CG2 A:THR576 3.9 39.0 1.0
N A:LEU580 4.1 68.7 1.0
CB A:ASP574 4.1 37.6 1.0
CA A:LEU580 4.1 41.7 1.0
CA A:THR576 4.1 39.0 1.0
CB A:ASP582 4.2 40.6 1.0
O A:VAL581 4.2 44.0 1.0
C A:VAL581 4.2 53.6 1.0
CA A:ASP574 4.2 37.4 1.0
N A:LEU575 4.3 37.7 1.0
CB A:LEU580 4.3 38.7 1.0
OD2 A:ASP574 4.4 67.2 1.0
N A:ASP578 4.4 44.1 1.0
N A:VAL581 4.4 48.5 1.0
CB A:ASP578 4.4 48.2 1.0
C A:THR576 4.4 49.9 1.0
N A:ASP582 4.5 49.9 1.0
N A:GLN577 4.6 54.7 1.0
C A:ASP574 4.6 39.0 1.0
CB A:ARG595 4.6 39.3 1.0
CA A:VAL581 4.6 51.4 1.0
CA A:ASP582 4.8 37.9 1.0
N A:GLY579 4.8 46.7 1.0
CA A:ASP578 4.9 42.8 1.0
O A:THR576 4.9 50.6 1.0

Calcium binding site 2 out of 5 in 4neh

Go back to Calcium Binding Sites List in 4neh
Calcium binding site 2 out of 5 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1103

b:54.3
occ:1.00
 O A:LEU517 2.1 63.4 1.0
OD1 A:ASP519 2.3 48.5 1.0
OD1 A:ASN513 2.3 57.6 1.0
OD1 A:ASP515 2.4 45.9 1.0
OD1 A:ASP511 2.4 56.1 1.0
OD2 A:ASP519 2.4 51.7 1.0
O A:HOH1261 2.4 38.6 1.0
CG A:ASP519 2.7 49.9 1.0
CG A:ASP515 3.2 52.4 1.0
C A:LEU517 3.3 51.0 1.0
CG A:ASN513 3.3 55.6 1.0
OD2 A:ASP515 3.4 60.0 1.0
CG A:ASP511 3.6 61.0 1.0
ND2 A:ASN513 3.7 48.1 1.0
CA A:LEU517 4.0 51.3 1.0
CB A:LEU517 4.0 50.7 1.0
N A:LEU517 4.0 62.1 1.0
CB A:ASP519 4.1 36.9 1.0
CA A:ASP511 4.1 53.1 1.0
N A:VAL512 4.2 57.1 1.0
CB A:ASP511 4.3 54.3 1.0
N A:THR518 4.4 45.9 1.0
C A:THR518 4.4 41.2 1.0
N A:ASP519 4.4 38.4 1.0
N A:ASN513 4.4 49.7 1.0
ND1 A:HIS538 4.5 53.8 1.0
OD2 A:ASP511 4.5 74.9 1.0
N A:GLY539 4.5 55.2 1.0
CB A:ASP515 4.6 45.4 1.0
C A:ASP511 4.6 52.2 1.0
N A:ASP515 4.7 53.5 1.0
O A:THR518 4.7 52.0 1.0
CA A:THR518 4.7 35.8 1.0
CB A:ASN513 4.7 56.2 1.0
CA A:ASP519 4.7 38.9 1.0
CG A:HIS538 4.9 56.8 1.0

Calcium binding site 3 out of 5 in 4neh

Go back to Calcium Binding Sites List in 4neh
Calcium binding site 3 out of 5 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1104

b:0.0
occ:1.00
 OD1 A:ASP451 2.3 88.3 1.0
OD1 A:ASP455 2.3 1.0 1.0
OD1 A:ASP447 2.3 82.2 1.0
OD1 A:ASP449 2.4 84.0 1.0
OD2 A:ASP451 2.4 84.2 1.0
O A:HOH1311 2.4 99.7 1.0
O A:SER453 2.5 58.0 1.0
CG A:ASP451 2.5 80.3 1.0
OD2 A:ASP455 2.9 83.5 1.0
CG A:ASP455 2.9 76.2 1.0
CG A:ASP449 3.4 77.2 1.0
CG A:ASP447 3.5 72.5 1.0
C A:SER453 3.6 50.7 1.0
OD2 A:ASP449 3.8 78.7 1.0
CB A:ASP451 3.9 61.7 1.0
N A:ASP451 4.0 72.3 1.0
N A:SER453 4.1 68.9 1.0
CA A:SER453 4.2 52.6 1.0
OD2 A:ASP447 4.2 66.7 1.0
CB A:SER453 4.3 59.5 1.0
CB A:ASP455 4.4 48.8 1.0
CA A:ASP451 4.4 63.8 1.0
N A:ASP449 4.5 55.6 1.0
N A:ASP455 4.5 47.5 1.0
CA A:ASP447 4.6 49.5 1.0
N A:SER450 4.6 70.1 1.0
CB A:ASP447 4.6 56.6 1.0
N A:VAL448 4.7 47.0 1.0
N A:THR454 4.7 48.9 1.0
C A:ASP447 4.7 49.8 1.0
N A:GLY452 4.7 66.9 1.0
CB A:ASP449 4.7 69.8 1.0
C A:THR454 4.8 47.6 1.0
CA A:ASP455 4.8 52.7 1.0
C A:ASP451 4.9 64.5 1.0
C A:ASP449 4.9 71.7 1.0
CA A:ASP449 5.0 63.0 1.0

Calcium binding site 4 out of 5 in 4neh

Go back to Calcium Binding Sites List in 4neh
Calcium binding site 4 out of 5 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca701

b:48.5
occ:1.00
 O B:PRO211 2.2 50.0 1.0
OD1 B:ASP209 2.3 70.8 1.0
OD1 B:ASN207 2.3 57.2 1.0
OE2 B:GLU212 2.4 56.4 1.0
OD2 B:ASP151 2.4 66.3 1.0
O B:ASP209 2.4 59.0 1.0
C B:PRO211 3.3 49.0 1.0
CG B:ASP209 3.3 63.9 1.0
C B:ASP209 3.4 45.7 1.0
CG B:ASN207 3.4 68.0 1.0
CD B:GLU212 3.5 53.6 1.0
CG B:ASP151 3.5 62.0 1.0
CA B:GLU212 3.7 43.7 1.0
OD2 B:ASP209 3.9 67.0 1.0
CB B:ASP151 3.9 57.4 1.0
N B:GLU212 3.9 48.7 1.0
ND2 B:ASN207 3.9 69.7 1.0
NE2 B:HIS246 4.1 50.5 1.0
C B:ALA210 4.1 58.5 1.0
CA B:ASP209 4.1 40.6 1.0
O B:ALA210 4.1 62.7 1.0
N B:ASP209 4.1 50.0 1.0
OE1 B:GLU212 4.2 58.2 1.0
N B:PRO211 4.2 56.5 1.0
CB B:ASP209 4.3 56.6 1.0
N B:ALA210 4.3 45.4 1.0
CA B:PRO211 4.4 46.2 1.0
CD2 B:HIS246 4.4 41.6 1.0
O B:PHE157 4.4 46.8 1.0
CG B:GLU212 4.4 43.1 1.0
CB B:GLU212 4.5 45.7 1.0
OD1 B:ASP151 4.6 54.6 1.0
CA B:ALA210 4.6 50.8 1.0
CB B:ASN207 4.7 58.5 1.0
C B:GLU212 4.8 60.9 1.0
CD B:PRO211 4.9 48.1 1.0

Calcium binding site 5 out of 5 in 4neh

Go back to Calcium Binding Sites List in 4neh
Calcium binding site 5 out of 5 in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca702

b:0.2
occ:1.00
 O B:HOH861 2.3 96.9 1.0
O B:HOH812 2.4 66.3 1.0
O B:GLU325 2.4 90.2 1.0
O B:HOH860 2.4 65.3 1.0
OD1 B:ASP120 2.4 0.2 1.0
OD2 B:ASP120 2.4 93.7 1.0
O B:HOH809 2.4 76.8 1.0
CG B:ASP120 2.6 92.1 1.0
C B:GLU325 3.5 78.5 1.0
CB B:ASP120 3.9 75.0 1.0
CA B:GLU325 4.0 74.5 1.0
N B:ASP120 4.1 88.6 1.0
O B:SER116 4.1 73.5 1.0
O B:HOH830 4.4 60.9 1.0
CB B:GLU325 4.4 71.9 1.0
O B:HOH829 4.4 56.9 1.0
CA B:ASP120 4.5 84.2 1.0
CA B:MET117 4.5 55.4 1.0
N B:ASP326 4.6 72.9 1.0
OE1 B:GLU325 4.7 99.2 1.0
CB B:ASP242 4.7 41.7 1.0
CB B:ASP119 4.8 96.8 1.0
SD B:MET117 4.8 59.8 1.0
OD2 B:ASP242 4.8 80.4 1.0
C B:ASP119 4.9 92.4 1.0
C B:MET117 4.9 55.0 1.0
CA B:ASP326 5.0 75.7 1.0
N B:ASP119 5.0 78.1 1.0

Reference:

M.Sen, K.Yuki, T.A.Springer. An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, Alpha X Beta 2. J.Cell Biol. V. 203 629 2013.
ISSN: ISSN 0021-9525
PubMed: 24385486
DOI: 10.1083/JCB.201308083
Page generated: Wed Jul 9 00:49:57 2025

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