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Calcium in PDB 4k2p: The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain

Protein crystallography data

The structure of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain, PDB code: 4k2p was solved by M.Joshi, L.Gakhar, E.J.Fuentes, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.70 / 1.98
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.507, 70.111, 87.753, 90.00, 90.19, 90.00
R / Rfree (%) 19.2 / 23.6

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain (pdb code 4k2p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 5 binding sites of Calcium where determined in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain, PDB code: 4k2p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5;

Calcium binding site 1 out of 5 in 4k2p

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Calcium binding site 1 out of 5 in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1001

b:53.2
occ:1.00
 OD1 A:ASN610 2.3 25.8 1.0
O A:HOH1117 2.4 35.5 1.0
O A:HOH1238 2.4 45.3 1.0
O A:HOH1149 2.4 47.0 1.0
O A:HOH1187 2.4 39.9 1.0
O A:HOH1144 2.5 40.0 1.0
CG A:ASN610 3.5 26.4 1.0
HG13 A:VAL606 3.8 35.0 1.0
HA A:ASN610 4.0 27.7 1.0
HD21 A:ASN610 4.0 37.4 1.0
ND2 A:ASN610 4.2 31.2 1.0
HB3 A:GLN609 4.3 45.3 1.0
HG2 A:GLN609 4.4 58.0 1.0
O A:HOH1241 4.5 32.1 1.0
CA A:ASN610 4.6 23.1 1.0
O A:HOH1285 4.6 47.4 1.0
CB A:ASN610 4.6 23.1 1.0
N A:ASN610 4.6 22.2 1.0
O A:VAL606 4.7 22.9 1.0
O A:HOH1261 4.7 47.0 1.0
H A:ASN610 4.7 26.6 1.0
CG1 A:VAL606 4.7 29.2 1.0
HG12 A:VAL606 4.7 35.0 1.0

Calcium binding site 2 out of 5 in 4k2p

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Calcium binding site 2 out of 5 in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1002

b:46.9
occ:1.00
 O A:GLU557 2.3 50.9 1.0
O A:HOH1289 2.3 25.7 1.0
O B:GLU557 2.3 47.7 1.0
O B:HOH1269 2.4 41.2 1.0
O B:HOH1266 2.4 38.1 1.0
O B:HOH1279 2.4 52.5 1.0
C A:GLU557 3.4 47.2 1.0
C B:GLU557 3.5 44.5 1.0
HA A:ASP558 3.5 52.9 1.0
HA B:ASP558 3.7 49.7 1.0
HB3 A:GLU557 3.8 64.5 1.0
HB3 B:GLU557 3.9 62.2 1.0
H A:THR559 3.9 47.1 1.0
H B:THR559 4.1 40.3 1.0
HA B:GLU557 4.2 54.9 1.0
HA A:GLU557 4.2 59.1 1.0
N A:ASP558 4.2 45.5 1.0
O A:HOH1167 4.3 51.1 1.0
CA A:GLU557 4.3 49.2 1.0
CA A:ASP558 4.3 44.1 1.0
CA B:GLU557 4.3 45.7 1.0
N B:ASP558 4.4 42.8 1.0
O B:HOH1265 4.4 24.8 1.0
CA B:ASP558 4.5 41.4 1.0
CB A:GLU557 4.5 53.8 1.0
O A:HOH1126 4.6 32.8 1.0
CB B:GLU557 4.6 51.9 1.0
OE1 A:GLU557 4.7 58.4 1.0
N A:THR559 4.7 39.3 1.0
O B:HOH1189 4.8 49.8 1.0
N B:THR559 4.9 33.6 1.0
CD A:GLU557 5.0 61.9 1.0
CD B:GLU557 5.0 66.6 1.0
OE1 B:GLU557 5.0 70.9 1.0

Calcium binding site 3 out of 5 in 4k2p

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Calcium binding site 3 out of 5 in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1001

b:45.5
occ:1.00
 O B:HOH1225 2.4 29.6 1.0
O B:HOH1295 2.4 45.4 1.0
OD1 B:ASN610 2.4 29.5 1.0
O B:HOH1280 2.4 45.4 1.0
O B:HOH1154 2.4 41.9 1.0
O B:HOH1188 2.5 48.8 1.0
O B:HOH1236 2.5 50.2 1.0
CG B:ASN610 3.6 26.9 1.0
HG13 B:VAL606 3.9 34.0 1.0
HA B:ASN610 4.0 24.4 1.0
HD21 B:ASN610 4.2 35.6 1.0
HB3 B:GLN609 4.4 41.2 1.0
O B:HOH1159 4.4 39.7 1.0
ND2 B:ASN610 4.4 29.7 1.0
CA B:ASN610 4.6 20.3 1.0
O B:VAL606 4.6 24.7 1.0
N B:ASN610 4.6 20.9 1.0
O B:HOH1185 4.6 48.2 1.0
HB2 B:GLN609 4.6 41.2 1.0
H B:ASN610 4.6 25.0 1.0
O B:HOH1230 4.7 46.0 1.0
CB B:ASN610 4.7 22.4 1.0
O B:HOH1149 4.7 38.5 1.0
CG1 B:VAL606 4.8 28.3 1.0
HG12 B:VAL606 4.8 34.0 1.0
CB B:GLN609 5.0 34.4 1.0
O B:HOH1249 5.0 32.3 1.0

Calcium binding site 4 out of 5 in 4k2p

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Calcium binding site 4 out of 5 in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1001

b:45.4
occ:1.00
 O C:HOH1299 2.4 54.0 1.0
OD1 C:ASN610 2.4 27.5 1.0
O C:HOH1160 2.4 32.5 1.0
O C:HOH1282 2.4 45.8 1.0
O C:HOH1263 2.4 48.5 1.0
O C:HOH1300 2.4 54.7 1.0
O C:HOH1281 2.5 49.1 1.0
CG C:ASN610 3.6 28.8 1.0
HG13 C:VAL606 3.9 38.4 1.0
HA C:ASN610 4.0 30.1 1.0
HD21 C:ASN610 4.2 37.5 1.0
HB3 C:GLN609 4.3 39.6 1.0
ND2 C:ASN610 4.3 31.2 1.0
O C:HOH1161 4.4 33.8 1.0
CA C:ASN610 4.6 25.1 1.0
O C:HOH1181 4.6 51.1 1.0
N C:ASN610 4.6 23.8 1.0
HB2 C:GLN609 4.6 39.6 1.0
O C:HOH1257 4.6 32.8 1.0
H C:ASN610 4.7 28.5 1.0
O C:HOH1200 4.7 46.9 1.0
CB C:ASN610 4.7 25.5 1.0
O C:VAL606 4.7 23.2 1.0
OE1 C:GLN609 4.8 58.6 1.0
CG1 C:VAL606 4.8 32.0 1.0
HG12 C:VAL606 4.8 38.4 1.0
CB C:GLN609 4.9 33.0 1.0

Calcium binding site 5 out of 5 in 4k2p

Go back to Calcium Binding Sites List in 4k2p
Calcium binding site 5 out of 5 in the The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of The Structure of A Quintuple Mutant of the TIAM1 pH-Cc-Ex Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca1001

b:45.6
occ:1.00
 O D:HOH1144 2.4 32.0 1.0
O D:HOH1218 2.4 50.1 1.0
O D:HOH1148 2.4 38.7 1.0
OD1 D:ASN610 2.4 25.5 1.0
O D:HOH1241 2.4 38.2 1.0
O D:HOH1117 2.4 42.5 1.0
O D:HOH1255 2.5 43.7 1.0
CG D:ASN610 3.6 24.9 1.0
HG13 D:VAL606 4.0 29.9 1.0
HA D:ASN610 4.0 26.3 1.0
HD21 D:ASN610 4.2 33.7 1.0
ND2 D:ASN610 4.3 28.1 1.0
HB3 D:GLN609 4.4 44.5 1.0
O D:HOH1254 4.4 53.3 1.0
O D:HOH1121 4.6 29.9 1.0
CA D:ASN610 4.6 21.9 1.0
N D:ASN610 4.7 23.8 1.0
HB2 D:GLN609 4.7 44.5 1.0
O D:VAL606 4.7 19.9 1.0
H D:ASN610 4.7 28.6 1.0
CB D:ASN610 4.7 22.8 1.0
O D:HOH1145 4.7 45.5 1.0
CG1 D:VAL606 4.8 24.9 1.0
HG12 D:VAL606 4.8 29.9 1.0

Reference:

M.Joshi, L.Gakhar, E.J.Fuentes. High-Resolution Structure of the TIAM1 Phn-Cc-Ex Domain. Acta Crystallogr.,Sect.F V. 69 744 2013.
ISSN: ESSN 1744-3091
PubMed: 23832200
DOI: 10.1107/S1744309113014206
Page generated: Tue Jul 8 23:20:08 2025

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