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Calcium in PDB 5f7h: Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine

Protein crystallography data

The structure of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine, PDB code: 5f7h was solved by G.F.Gao, G.Lu, H.Wang, J.Qi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 212.444, 65.034, 68.851, 90.00, 108.55, 90.00
R / Rfree (%) 21 / 27.8

Calcium Binding Sites:

The binding sites of Calcium atom in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine (pdb code 5f7h). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine, PDB code: 5f7h:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 1 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca201

b:44.1
occ:1.00
 O1P B:SEP202 2.1 31.8 1.0
O B:VAL95 2.2 39.2 1.0
OD1 B:ASN100 2.4 40.8 1.0
O B:GLY97 2.4 44.3 1.0
OD1 B:ASP101 2.6 35.0 1.0
O A:HOH316 2.8 42.7 1.0
P B:SEP202 3.3 37.1 1.0
O2P B:SEP202 3.4 45.5 1.0
C B:VAL95 3.4 38.9 1.0
CG B:ASP101 3.5 35.7 1.0
C B:GLY97 3.5 36.4 1.0
CG B:ASN100 3.5 38.6 1.0
N B:VAL95 3.9 36.0 1.0
OD2 B:ASP101 4.0 37.7 1.0
ND2 B:ASN100 4.1 37.9 1.0
O3P B:SEP202 4.1 46.5 1.0
N B:ASP101 4.1 35.8 1.0
N B:GLY97 4.2 43.1 1.0
CA B:VAL95 4.2 32.8 1.0
C B:PRO96 4.2 39.6 1.0
CA B:TRP98 4.3 35.9 1.0
N B:TRP98 4.3 38.9 1.0
N B:PRO96 4.4 37.5 1.0
O B:HOH305 4.4 42.2 1.0
CA B:GLY97 4.4 36.6 1.0
N B:ASN100 4.5 40.1 1.0
OG B:SEP202 4.5 50.4 1.0
C B:ASN100 4.5 37.5 1.0
CB B:ASP101 4.5 35.5 1.0
CA B:PRO96 4.5 34.8 1.0
O B:PRO96 4.6 44.7 1.0
CA B:ASP101 4.6 38.6 1.0
CB B:VAL95 4.6 38.5 1.0
C B:TRP98 4.7 36.5 1.0
CB B:ASN100 4.8 27.1 1.0
OE1 A:GLU83 4.8 57.8 1.0
CA B:ASN100 4.8 33.6 1.0
N B:PHE99 4.8 30.6 1.0
CD1 B:TRP98 4.9 42.3 1.0

Calcium binding site 2 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 2 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca201

b:43.8
occ:1.00
 O3P A:SEP202 2.1 38.6 1.0
O A:VAL95 2.2 38.1 1.0
O A:GLY97 2.3 47.5 1.0
OD1 A:ASN100 2.4 49.7 1.0
OD1 A:ASP101 2.6 41.9 1.0
P A:SEP202 3.2 35.8 1.0
O2P A:SEP202 3.3 46.8 1.0
CG A:ASP101 3.4 43.9 1.0
C A:VAL95 3.4 38.9 1.0
C A:GLY97 3.5 41.5 1.0
CG A:ASN100 3.6 44.0 1.0
O1P A:SEP202 3.9 40.9 1.0
OD2 A:ASP101 3.9 41.7 1.0
O A:HOH309 4.0 40.2 1.0
N A:VAL95 4.0 40.0 1.0
N A:ASP101 4.0 38.1 1.0
ND2 A:ASN100 4.1 40.5 1.0
CA A:VAL95 4.2 40.0 1.0
N A:GLY97 4.2 48.4 1.0
CA A:TRP98 4.2 39.4 1.0
N A:TRP98 4.3 41.1 1.0
C A:PRO96 4.3 45.8 1.0
N A:PRO96 4.5 35.8 1.0
CB A:ASP101 4.5 45.3 1.0
CA A:GLY97 4.5 40.8 1.0
OG A:SEP202 4.5 50.4 1.0
N A:ASN100 4.5 39.7 1.0
CA A:ASP101 4.6 40.5 1.0
C A:ASN100 4.6 46.0 1.0
CB A:VAL95 4.6 41.6 1.0
C A:TRP98 4.6 39.3 1.0
CA A:PRO96 4.6 40.3 1.0
O A:PRO96 4.7 46.0 1.0
N A:PHE99 4.7 40.0 1.0
CB A:ASN100 4.8 36.0 1.0
CA A:ASN100 4.9 37.9 1.0
CD1 A:TRP98 4.9 39.8 1.0

Calcium binding site 3 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 3 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca201

b:61.7
occ:1.00
 O1P C:SEP202 2.1 61.8 1.0
O C:HOH302 2.3 53.0 1.0
O C:VAL95 2.6 53.7 1.0
OD1 C:ASN100 2.6 63.2 1.0
O C:GLY97 2.8 71.1 1.0
OD1 C:ASP101 2.9 48.7 1.0
P C:SEP202 3.1 75.1 1.0
O2P C:SEP202 3.2 57.9 1.0
C C:GLY97 3.4 71.4 1.0
CG C:ASP101 3.6 47.7 1.0
O3P C:SEP202 3.6 77.4 1.0
CG C:ASN100 3.8 66.8 1.0
C C:VAL95 3.8 56.3 1.0
N C:TRP98 3.9 68.3 1.0
CA C:TRP98 3.9 68.8 1.0
OD2 C:ASP101 4.1 48.0 1.0
N C:GLY97 4.2 65.1 1.0
N C:ASP101 4.2 56.1 1.0
CA C:GLY97 4.3 68.0 1.0
N C:VAL95 4.4 47.4 1.0
ND2 C:ASN100 4.4 63.9 1.0
N C:PHE99 4.5 68.4 1.0
OG C:SEP202 4.5 69.4 1.0
N C:ASN100 4.5 65.9 1.0
CB C:ASP101 4.5 47.0 1.0
C C:TRP98 4.5 72.0 1.0
C C:PRO96 4.5 65.1 1.0
CA C:VAL95 4.6 55.0 1.0
CE3 C:TRP98 4.6 82.2 1.0
C C:ASN100 4.7 62.6 1.0
CA C:ASP101 4.7 50.8 1.0
N C:PRO96 4.8 62.9 1.0
CB C:VAL95 4.9 56.5 1.0
O C:PRO96 4.9 69.7 1.0
CA C:ASN100 4.9 62.2 1.0
CB C:ASN100 5.0 56.4 1.0
CA C:PRO96 5.0 60.3 1.0

Calcium binding site 4 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 4 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca201

b:65.7
occ:1.00
 O D:VAL95 2.5 58.7 1.0
OD1 D:ASN100 2.6 59.4 1.0
O2P D:SEP202 2.7 59.6 1.0
OD1 D:ASP101 2.7 56.3 1.0
O3P D:SEP202 2.9 81.2 1.0
O D:GLY97 3.0 68.7 1.0
P D:SEP202 3.0 72.4 1.0
O1P D:SEP202 3.2 77.6 1.0
CG D:ASP101 3.4 58.1 1.0
C D:GLY97 3.5 68.1 1.0
C D:VAL95 3.7 62.1 1.0
CG D:ASN100 3.7 60.3 1.0
OD2 D:ASP101 3.8 62.0 1.0
N D:GLY97 3.9 59.6 1.0
ND2 D:ASN100 4.2 64.3 1.0
CA D:GLY97 4.2 64.1 1.0
N D:VAL95 4.2 50.3 1.0
N D:TRP98 4.2 74.8 1.0
N D:ASP101 4.3 56.9 1.0
CA D:TRP98 4.3 78.2 1.0
C D:PRO96 4.5 61.0 1.0
CA D:VAL95 4.5 57.5 1.0
CB D:ASP101 4.5 56.3 1.0
OG D:SEP202 4.6 80.5 1.0
N D:PRO96 4.6 65.7 1.0
N D:ASN100 4.7 61.0 1.0
CA D:ASP101 4.8 58.5 1.0
C D:TRP98 4.8 74.3 1.0
CA D:PRO96 4.8 66.1 1.0
N D:PHE99 4.8 74.0 1.0
CD1 D:TRP98 4.9 96.2 1.0
C D:ASN100 4.9 59.5 1.0
OG D:SER41 5.0 65.9 1.0
CB D:ASN100 5.0 54.1 1.0
CB D:VAL95 5.0 57.2 1.0

Calcium binding site 5 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 5 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca201

b:50.0
occ:1.00
 OD1 E:ASN100 2.3 45.6 1.0
O E:HOH308 2.4 40.1 1.0
O E:VAL95 2.4 54.0 1.0
O1P E:SEP202 2.4 48.0 1.0
OD1 E:ASP101 2.6 46.8 1.0
O2P E:SEP202 2.6 52.9 1.0
O E:GLY97 2.8 56.9 1.0
P E:SEP202 3.1 52.8 1.0
CG E:ASP101 3.3 50.6 1.0
C E:GLY97 3.4 54.7 1.0
CG E:ASN100 3.5 52.8 1.0
C E:VAL95 3.6 54.2 1.0
OD2 E:ASP101 3.8 52.2 1.0
N E:GLY97 3.9 56.1 1.0
O3P E:SEP202 3.9 62.0 1.0
N E:ASP101 4.0 48.2 1.0
N E:VAL95 4.0 48.8 1.0
N E:TRP98 4.2 57.2 1.0
CA E:GLY97 4.2 53.4 1.0
CB E:ASP101 4.2 53.2 1.0
ND2 E:ASN100 4.2 52.8 1.0
N E:ASN100 4.3 49.5 1.0
CA E:VAL95 4.3 54.3 1.0
CA E:TRP98 4.3 59.3 1.0
C E:ASN100 4.4 54.1 1.0
CA E:ASP101 4.4 52.4 1.0
OG E:SEP202 4.4 60.2 1.0
C E:PRO96 4.4 54.9 1.0
N E:PRO96 4.6 57.6 1.0
C E:TRP98 4.6 52.9 1.0
CB E:VAL95 4.6 57.7 1.0
CA E:ASN100 4.6 50.3 1.0
CB E:ASN100 4.7 54.6 1.0
CA E:PRO96 4.8 53.1 1.0
OG E:SER41 4.8 63.7 1.0
N E:PHE99 4.8 53.4 1.0
O E:ASN100 5.0 58.4 1.0

Calcium binding site 6 out of 6 in 5f7h

Go back to Calcium Binding Sites List in 5f7h
Calcium binding site 6 out of 6 in the Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Human T-Cell Immunoglobulin and Mucin Domain Protein 4 (Htim-4) Complex with Phosphoserine within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca201

b:60.9
occ:1.00
 OD1 F:ASP101 2.4 55.1 1.0
O F:GLY97 2.5 70.7 1.0
O F:VAL95 2.5 67.5 1.0
OD1 F:ASN100 2.5 60.4 1.0
O1P F:SEP202 2.8 72.5 1.0
O3P F:SEP202 3.0 50.8 1.0
P F:SEP202 3.3 65.3 1.0
C F:GLY97 3.3 65.7 1.0
CG F:ASP101 3.4 56.6 1.0
O2P F:SEP202 3.5 68.4 1.0
C F:VAL95 3.6 60.3 1.0
CA F:TRP98 3.7 69.1 1.0
CG F:ASN100 3.7 58.4 1.0
N F:TRP98 3.8 64.1 1.0
N F:VAL95 4.0 59.2 1.0
OD2 F:ASP101 4.0 56.9 1.0
N F:ASP101 4.0 58.2 1.0
CA F:VAL95 4.2 55.4 1.0
N F:GLY97 4.3 62.8 1.0
CB F:ASP101 4.3 53.5 1.0
ND2 F:ASN100 4.3 57.3 1.0
CA F:GLY97 4.3 64.5 1.0
C F:TRP98 4.4 68.2 1.0
CA F:ASP101 4.5 56.7 1.0
N F:ASN100 4.5 62.4 1.0
CB F:VAL95 4.5 55.6 1.0
C F:PRO96 4.5 62.9 1.0
C F:ASN100 4.7 56.8 1.0
N F:PRO96 4.7 62.9 1.0
N F:PHE99 4.7 65.8 1.0
OG F:SEP202 4.8 82.0 1.0
CB F:TRP98 4.8 67.1 1.0
CA F:ASN100 4.9 57.9 1.0
CB F:ASN100 4.9 52.9 1.0
O F:PRO96 4.9 60.6 1.0
CA F:PRO96 5.0 61.3 1.0

Reference:

H.Wang, J.X.Qi, N.N.Liu. Crystal Structures of Human Tim Members: Ebolavirus Entry-Enhancing Receptors Chin.Sci.Bull. V. 60 3438 2015.
ISSN: ISSN 1001-6538
DOI: 10.1360/N972015-01255
Page generated: Sun Jul 14 19:07:50 2024

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