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Calcium in PDB 5k89: Crystal Structure of Human Calcium-Bound S100A1

Protein crystallography data

The structure of Crystal Structure of Human Calcium-Bound S100A1, PDB code: 5k89 was solved by Z.Melville, E.Aligholizadeh, L.E.Mcknight, D.Weber, E.Pozharski, D.J.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.64 / 2.25
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 53.547, 53.547, 193.387, 90.00, 90.00, 120.00
R / Rfree (%) 27.5 / 29.1

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Human Calcium-Bound S100A1 (pdb code 5k89). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Human Calcium-Bound S100A1, PDB code: 5k89:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5k89

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Calcium binding site 1 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


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 Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca102

b:71.0
occ:1.00
 O A:GLU69 2.3 79.9 1.0
OD1 A:ASN65 2.3 0.5 1.0
OD2 A:ASP67 2.4 97.9 1.0
OE1 A:GLU74 2.5 68.0 1.0
OD1 A:ASP63 2.6 95.6 1.0
OE2 A:GLU74 3.0 82.9 1.0
CD A:GLU74 3.1 83.3 1.0
CG A:ASP67 3.1 0.3 1.0
OD1 A:ASP67 3.1 98.6 1.0
CG A:ASN65 3.2 0.3 1.0
ND2 A:ASN65 3.4 0.6 1.0
C A:GLU69 3.5 77.0 1.0
CG A:ASP63 3.6 96.1 1.0
OD1 A:ASP71 3.7 89.5 1.0
CA A:VAL70 4.2 67.7 1.0
CA A:ASP63 4.2 83.5 1.0
N A:VAL70 4.3 70.0 1.0
N A:ASP71 4.3 69.4 1.0
N A:GLU69 4.4 83.3 1.0
OD2 A:ASP63 4.4 0.8 1.0
CG A:ASP71 4.4 85.3 1.0
CB A:ASP63 4.4 88.2 1.0
N A:ASP67 4.5 0.6 1.0
CA A:GLU69 4.5 77.4 1.0
CB A:ASP67 4.5 0.8 1.0
CG A:GLU74 4.5 78.0 1.0
N A:ASN65 4.5 95.4 1.0
N A:GLY66 4.6 99.0 1.0
CB A:ASN65 4.6 0.1 1.0
C A:ASP63 4.7 88.8 1.0
C A:VAL70 4.7 69.0 1.0
N A:GLU64 4.8 84.9 1.0
CA A:ASN65 5.0 0.7 1.0
OD2 A:ASP71 5.0 89.2 1.0

Calcium binding site 2 out of 6 in 5k89

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Calcium binding site 2 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


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 Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca103

b:60.1
occ:1.00
 O A:HOH202 2.2 41.3 1.0
OE2 A:GLU33 2.3 61.5 1.0
O A:GLU23 2.4 81.0 1.0
O A:SER20 2.4 68.9 1.0
O A:ASP25 2.5 80.3 1.0
O A:LYS28 2.6 74.6 1.0
OE1 A:GLU33 2.6 63.9 1.0
CD A:GLU33 2.8 68.2 1.0
C A:SER20 3.5 65.1 1.0
C A:ASP25 3.5 83.8 1.0
C A:GLU23 3.5 84.9 1.0
C A:LYS28 3.8 74.5 1.0
N A:GLU23 4.0 76.3 1.0
N A:ASP25 4.0 89.6 1.0
CA A:SER20 4.1 59.3 1.0
C A:GLY24 4.2 91.3 1.0
CG A:GLU33 4.3 65.8 1.0
OE2 A:GLU69 4.3 89.9 1.0
N A:LYS26 4.3 80.7 1.0
OG A:SER20 4.3 74.3 1.0
CA A:ASP25 4.4 87.7 1.0
CA A:LYS26 4.4 75.5 1.0
N A:LYS22 4.4 68.0 1.0
CA A:GLU23 4.4 82.0 1.0
N A:GLY24 4.5 88.8 1.0
N A:SER30 4.5 74.2 1.0
N A:GLY21 4.5 62.1 1.0
CA A:GLY24 4.5 91.7 1.0
O A:GLY24 4.5 89.4 1.0
N A:LYS28 4.6 75.1 1.0
CA A:LEU29 4.6 67.2 1.0
N A:LEU29 4.7 70.0 1.0
CA A:GLY21 4.7 65.9 1.0
C A:LYS26 4.8 74.7 1.0
O A:HIS19 4.8 59.3 1.0
CA A:LYS28 4.8 75.7 1.0
CB A:SER20 4.9 61.8 1.0
C A:GLY21 4.9 71.0 1.0
C A:LEU29 5.0 74.5 1.0

Calcium binding site 3 out of 6 in 5k89

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Calcium binding site 3 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


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 Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:83.7
occ:1.00
 OD2 C:ASP63 2.3 87.5 1.0
O C:GLU69 2.4 92.0 1.0
OE2 C:GLU74 2.5 72.7 1.0
OD1 C:ASN65 2.7 0.9 1.0
OD1 C:ASP67 2.7 0.8 1.0
OE1 C:GLU74 2.9 78.1 1.0
O C:HOH201 2.9 60.9 1.0
CD C:GLU74 3.1 80.7 1.0
CG C:ASP63 3.4 89.1 1.0
CG C:ASN65 3.6 0.8 1.0
C C:GLU69 3.6 89.4 1.0
CG C:ASP67 3.6 0.8 1.0
CA C:ASP63 3.8 85.8 1.0
ND2 C:ASN65 3.8 0.9 1.0
OD2 C:ASP67 3.9 0.7 1.0
OD2 C:ASP71 4.1 96.1 1.0
CB C:ASP63 4.1 88.9 1.0
N C:GLU64 4.2 0.9 1.0
OD1 C:ASP63 4.3 90.8 1.0
C C:ASP63 4.3 87.7 1.0
CA C:VAL70 4.3 80.7 1.0
N C:VAL70 4.4 83.3 1.0
N C:ASP71 4.4 81.9 1.0
N C:ASP67 4.4 0.5 1.0
N C:GLU69 4.5 94.8 1.0
N C:GLY66 4.5 0.4 1.0
CG C:GLU74 4.6 74.4 1.0
N C:ASN65 4.6 0.8 1.0
CA C:GLU69 4.6 90.5 1.0
CG C:ASP71 4.7 88.9 1.0
C C:VAL70 4.9 79.8 1.0
CB C:ASP67 4.9 0.5 1.0
CB C:ASN65 4.9 0.8 1.0

Calcium binding site 4 out of 6 in 5k89

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Calcium binding site 4 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


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 Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca102

b:54.5
occ:1.00
 O C:SER20 2.3 79.8 1.0
O C:ASP25 2.4 87.5 1.0
O C:LYS28 2.5 80.2 1.0
O C:GLU23 2.5 88.5 1.0
OE1 C:GLU33 2.5 71.7 1.0
OE2 C:GLU33 2.8 73.5 1.0
CD C:GLU33 3.0 71.5 1.0
C C:ASP25 3.4 91.0 1.0
C C:SER20 3.5 77.1 1.0
C C:GLU23 3.7 91.1 1.0
C C:LYS28 3.7 79.5 1.0
N C:GLU23 4.0 86.4 1.0
OG C:SER20 4.0 77.0 1.0
CA C:LYS26 4.2 89.0 1.0
CA C:SER20 4.2 73.3 1.0
N C:ASP25 4.2 95.2 1.0
N C:LYS26 4.2 92.1 1.0
OE2 C:GLU69 4.3 93.8 1.0
C C:GLY24 4.4 96.3 1.0
CA C:ASP25 4.4 94.7 1.0
N C:LYS22 4.4 81.8 1.0
CA C:GLU23 4.4 89.8 1.0
N C:LYS28 4.4 83.3 1.0
CG C:GLU33 4.5 69.3 1.0
N C:GLY21 4.5 77.7 1.0
N C:SER30 4.5 72.4 1.0
C C:LYS26 4.6 86.3 1.0
O C:GLY24 4.6 96.8 1.0
CA C:GLY21 4.6 81.9 1.0
CA C:LEU29 4.6 68.8 1.0
N C:LEU29 4.6 70.7 1.0
CA C:LYS28 4.6 82.0 1.0
N C:GLY24 4.7 95.5 1.0
O C:HOH204 4.7 65.7 1.0
CB C:SER20 4.8 73.8 1.0
N C:TYR27 4.9 87.1 1.0
C C:GLY21 4.9 83.3 1.0
CA C:GLY24 4.9 97.3 1.0
CB C:ASP25 4.9 94.4 1.0
CB C:GLU23 4.9 88.6 1.0

Calcium binding site 5 out of 6 in 5k89

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Calcium binding site 5 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Human Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca101

b:92.9
occ:1.00
 O H:GLU69 2.3 0.3 1.0
OD1 H:ASN65 2.3 1.0 1.0
OD2 H:ASP63 2.3 0.2 1.0
OD2 H:ASP67 2.3 0.7 1.0
OE2 H:GLU74 2.7 0.1 1.0
CG H:ASN65 2.9 0.1 1.0
ND2 H:ASN65 2.9 0.2 1.0
OE1 H:GLU74 3.2 0.5 1.0
CD H:GLU74 3.3 0.7 1.0
CG H:ASP67 3.3 0.0 1.0
CG H:ASP63 3.4 0.8 1.0
C H:GLU69 3.5 0.6 1.0
OD1 H:ASP67 3.6 0.7 1.0
OD2 H:ASP71 3.9 0.5 1.0
OD1 H:ASP63 4.0 0.3 1.0
N H:ASP67 4.2 0.3 1.0
N H:GLU69 4.3 0.2 1.0
CB H:ASN65 4.4 0.7 1.0
CA H:VAL70 4.4 95.1 1.0
N H:VAL70 4.4 98.8 1.0
N H:ASP71 4.4 93.2 1.0
CB H:ASP63 4.4 0.6 1.0
N H:GLY66 4.4 0.7 1.0
CA H:ASP63 4.5 0.4 1.0
CA H:GLU69 4.5 0.9 1.0
N H:ASN65 4.6 0.9 1.0
CB H:ASP67 4.6 0.8 1.0
CG H:ASP71 4.6 0.1 1.0
CG H:GLU74 4.8 0.7 1.0
C H:VAL70 4.8 93.8 1.0
CA H:ASP67 4.9 0.3 1.0
N H:GLY68 4.9 0.6 1.0
CA H:ASN65 4.9 0.8 1.0
C H:ASP63 4.9 0.8 1.0
N H:GLU64 5.0 0.8 1.0

Calcium binding site 6 out of 6 in 5k89

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Calcium binding site 6 out of 6 in the Crystal Structure of Human Calcium-Bound S100A1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Human Calcium-Bound S100A1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca102

b:0.8
occ:1.00
 O H:GLU23 2.2 0.6 1.0
O H:SER20 2.3 91.8 1.0
O H:HOH201 2.3 77.7 1.0
OE2 H:GLU33 2.4 89.7 1.0
OE1 H:GLU33 2.4 87.2 1.0
O H:ASP25 2.4 97.9 1.0
CD H:GLU33 2.7 91.1 1.0
O H:LYS28 3.0 89.3 1.0
C H:GLU23 3.3 0.7 1.0
C H:SER20 3.4 88.2 1.0
N H:GLU23 3.4 0.7 1.0
C H:ASP25 3.6 0.6 1.0
N H:LYS22 3.9 96.7 1.0
CA H:GLU23 4.0 0.6 1.0
N H:ASP25 4.2 0.7 1.0
CG H:GLU33 4.2 89.0 1.0
CA H:SER20 4.2 83.9 1.0
C H:GLY24 4.2 0.5 1.0
C H:LYS28 4.2 86.3 1.0
N H:GLY21 4.3 88.6 1.0
CG H:GLU23 4.4 0.5 1.0
O H:GLY24 4.4 0.7 1.0
N H:GLY24 4.4 0.1 1.0
CA H:GLY21 4.4 93.1 1.0
CA H:LYS26 4.4 95.6 1.0
C H:LYS22 4.4 1.0 1.0
C H:GLY21 4.4 97.4 1.0
N H:LYS26 4.5 99.6 1.0
CA H:ASP25 4.5 0.8 1.0
OE1 H:GLU69 4.5 0.8 1.0
N H:SER30 4.6 92.4 1.0
OG H:SER20 4.6 91.3 1.0
O H:HIS19 4.7 86.9 1.0
CA H:LYS22 4.7 0.4 1.0
CA H:GLY24 4.7 0.3 1.0
CB H:GLU23 4.8 0.7 1.0
CA H:LEU29 4.9 83.3 1.0

Reference:

Z.Melville, E.Aligholizadeh, L.E.Mcknight, D.J.Weber, E.Pozharski, D.J.Weber. X-Ray Crystal Structure of Human Calcium-Bound S100A1. Acta Crystallogr F Struct V. 73 215 2017BIOL Commun.
ISSN: ESSN 2053-230X
PubMed: 28368280
DOI: 10.1107/S2053230X17003983
Page generated: Mon Jul 15 06:43:19 2024

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