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Calcium in PDB 4nen: 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: 4nen 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) 47.81 / 2.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 127.087, 119.851, 182.399, 90.00, 90.00, 90.00
R / Rfree (%) 22.4 / 26.4

Other elements in 4nen:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the An Internal Ligand-Bound, Metastable State of A Leukocyte Integrin, AXB2 (pdb code 4nen). 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: 4nen:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4nen

Go back to Calcium Binding Sites List in 4nen
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:Ca1113

b:54.5
occ:1.00
 O A:LEU517 2.2 58.9 1.0
OD1 A:ASN513 2.3 47.2 1.0
OD1 A:ASP511 2.3 73.7 1.0
OD2 A:ASP519 2.3 61.3 1.0
OD1 A:ASP519 2.4 56.7 1.0
O A:HOH1219 2.4 55.0 1.0
OD1 A:ASP515 2.4 71.2 1.0
CG A:ASP519 2.6 56.2 1.0
CG A:ASP515 3.1 79.7 1.0
OD2 A:ASP515 3.3 89.0 1.0
CG A:ASP511 3.3 61.5 1.0
CG A:ASN513 3.4 53.2 1.0
C A:LEU517 3.4 60.9 1.0
CA A:ASP511 3.6 54.6 1.0
CB A:ASP511 3.8 54.8 1.0
N A:VAL512 3.9 53.5 1.0
ND2 A:ASN513 4.0 55.8 1.0
CB A:ASP519 4.1 42.8 1.0
N A:ASN513 4.1 44.4 1.0
N A:LEU517 4.1 74.8 1.0
C A:ASP511 4.2 55.8 1.0
CA A:LEU517 4.2 64.9 1.0
N A:ASP519 4.2 40.8 1.0
OD2 A:ASP511 4.3 61.6 1.0
C A:THR518 4.3 53.2 1.0
N A:ASP515 4.3 70.2 1.0
N A:THR518 4.4 54.3 1.0
CB A:LEU517 4.4 56.2 1.0
ND1 A:HIS538 4.5 43.5 1.0
CB A:ASP515 4.5 78.1 1.0
CB A:ASN513 4.6 49.5 1.0
N A:GLY514 4.6 85.8 1.0
N A:GLY539 4.6 45.6 1.0
CA A:THR518 4.6 47.8 1.0
CA A:ASP519 4.6 40.4 1.0
O A:THR518 4.8 68.5 1.0
CA A:ASN513 4.8 45.5 1.0
N A:ASP511 4.8 63.6 1.0
CA A:ASP515 4.9 70.8 1.0
O A:GLY510 4.9 59.0 1.0
C A:ASN513 5.0 58.1 1.0

Calcium binding site 2 out of 5 in 4nen

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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:Ca1114

b:65.7
occ:1.00
 O A:LEU580 2.0 71.4 1.0
OD1 A:ASP578 2.2 70.9 1.0
OD1 A:ASP574 2.3 70.2 1.0
OG1 A:THR576 2.4 67.9 1.0
O A:HOH1225 2.4 39.8 1.0
OD2 A:ASP582 2.5 80.1 1.0
OD1 A:ASP582 2.9 67.2 1.0
CG A:ASP582 3.0 67.4 1.0
C A:LEU580 3.1 61.0 1.0
CG A:ASP574 3.3 77.7 1.0
CG A:ASP578 3.3 74.2 1.0
N A:LEU580 3.3 68.6 1.0
CA A:LEU580 3.6 56.7 1.0
CB A:THR576 3.7 62.4 1.0
OD2 A:ASP578 3.8 76.5 1.0
N A:THR576 3.8 65.7 1.0
CB A:LEU580 3.9 60.4 1.0
CB A:ASP574 3.9 72.4 1.0
N A:ASP578 4.0 63.5 1.0
CA A:ASP574 4.1 62.0 1.0
N A:GLY579 4.1 53.2 1.0
CA A:THR576 4.1 63.9 1.0
OD2 A:ASP574 4.2 86.9 1.0
N A:LEU575 4.2 52.4 1.0
N A:VAL581 4.3 59.4 1.0
N A:GLN577 4.3 71.0 1.0
C A:THR576 4.3 76.7 1.0
C A:GLY579 4.3 68.9 1.0
CB A:ASP582 4.5 47.9 1.0
C A:VAL581 4.5 40.5 1.0
CB A:ASP578 4.5 69.8 1.0
C A:ASP578 4.5 56.8 1.0
C A:ASP574 4.5 55.4 1.0
CG2 A:THR576 4.5 61.7 1.0
CA A:ASP578 4.6 66.6 1.0
O A:VAL581 4.6 40.9 1.0
CA A:VAL581 4.7 45.4 1.0
N A:ASP582 4.7 40.3 1.0
CA A:GLY579 4.7 58.9 1.0
O A:THR576 4.9 80.7 1.0
C A:LEU575 5.0 64.2 1.0

Calcium binding site 3 out of 5 in 4nen

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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:Ca1115

b:0.4
occ:1.00
 OD1 A:ASP451 2.3 86.6 1.0
OD1 A:ASP455 2.3 90.5 1.0
OD2 A:ASP455 2.3 63.9 1.0
OD1 A:ASP449 2.3 69.3 1.0
OD1 A:ASP447 2.3 67.5 1.0
O A:SER453 2.3 71.7 1.0
CG A:ASP455 2.6 73.6 1.0
CG A:ASP451 3.2 86.4 1.0
CG A:ASP449 3.4 60.9 1.0
CG A:ASP447 3.5 68.7 1.0
C A:SER453 3.5 63.9 1.0
OD2 A:ASP451 3.5 89.2 1.0
OD2 A:ASP449 3.8 64.6 1.0
CB A:ASP455 4.0 60.7 1.0
OD2 A:ASP447 4.2 70.6 1.0
CA A:SER453 4.2 61.9 1.0
N A:SER453 4.2 64.4 1.0
N A:ASP449 4.3 44.9 1.0
N A:ASP455 4.3 41.1 1.0
CB A:SER453 4.3 62.5 1.0
N A:ASP451 4.4 64.5 1.0
N A:VAL448 4.4 56.1 1.0
CB A:ASP451 4.5 83.3 1.0
C A:THR454 4.5 52.9 1.0
N A:THR454 4.6 63.2 1.0
CA A:ASP447 4.6 58.4 1.0
CB A:ASP447 4.6 61.0 1.0
N A:SER450 4.6 56.7 1.0
CB A:ASP449 4.6 51.5 1.0
CA A:ASP455 4.7 51.3 1.0
C A:ASP447 4.8 57.0 1.0
CA A:THR454 4.8 52.4 1.0
CA A:ASP449 4.8 45.5 1.0
CA A:ASP451 4.9 67.1 1.0
C A:ASP449 5.0 45.7 1.0

Calcium binding site 4 out of 5 in 4nen

Go back to Calcium Binding Sites List in 4nen
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:Ca705

b:44.6
occ:1.00
 OD1 B:ASN207 2.3 45.3 1.0
OD1 B:ASP209 2.3 36.7 1.0
O B:PRO211 2.3 33.6 1.0
O B:ASP209 2.3 35.1 1.0
OD2 B:ASP151 2.4 41.5 1.0
OE1 B:GLU212 2.4 56.7 1.0
CG B:ASN207 3.3 43.8 1.0
C B:PRO211 3.4 34.5 1.0
C B:ASP209 3.4 35.8 1.0
CD B:GLU212 3.4 47.2 1.0
CG B:ASP209 3.4 48.2 1.0
CG B:ASP151 3.5 42.5 1.0
ND2 B:ASN207 3.7 46.3 1.0
CA B:GLU212 3.7 36.5 1.0
CB B:ASP151 4.0 36.9 1.0
N B:GLU212 4.0 38.3 1.0
N B:ASP209 4.0 38.9 1.0
CA B:ASP209 4.1 40.9 1.0
O B:ALA210 4.1 37.0 1.0
OE2 B:GLU212 4.2 56.0 1.0
C B:ALA210 4.2 39.0 1.0
OD2 B:ASP209 4.2 51.0 1.0
CG B:GLU212 4.3 37.5 1.0
CB B:GLU212 4.3 33.7 1.0
CB B:ASP209 4.4 44.6 1.0
N B:ALA210 4.4 36.1 1.0
N B:PRO211 4.4 30.4 1.0
O B:PHE157 4.4 46.0 1.0
NE2 B:HIS246 4.4 45.0 1.0
CA B:PRO211 4.5 31.8 1.0
OD1 B:ASP151 4.6 48.0 1.0
CB B:ASN207 4.6 39.5 1.0
CA B:ALA210 4.7 39.1 1.0
CD2 B:HIS246 4.7 39.2 1.0
C B:GLU212 4.8 43.0 1.0
O B:VAL150 5.0 46.6 1.0

Calcium binding site 5 out of 5 in 4nen

Go back to Calcium Binding Sites List in 4nen
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:Ca706

b:92.7
occ:1.00
 OD2 B:ASP242 2.4 54.4 1.0
O B:SER116 2.4 64.4 1.0
O B:HOH810 2.5 86.1 1.0
O B:HOH809 2.6 0.8 1.0
O B:HOH834 2.9 45.5 1.0
CG B:ASP242 3.3 54.7 1.0
C B:SER116 3.5 53.8 1.0
CB B:ASP242 3.5 52.8 1.0
OD2 B:ASP120 3.8 68.3 1.0
CA B:MET117 4.2 40.5 1.0
N B:MET117 4.2 44.5 1.0
CG B:ASP120 4.4 58.3 1.0
SD B:MET117 4.4 41.9 1.0
CA B:SER116 4.5 51.0 1.0
CB B:SER116 4.5 46.6 1.0
OD1 B:ASP242 4.5 49.8 1.0
OD1 B:ASP120 4.5 65.9 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: Sun Jul 14 11:03:03 2024

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