Calcium in PDB 5o32: The Structure of Complement Complex

Enzymatic activity of The Structure of Complement Complex

All present enzymatic activity of The Structure of Complement Complex:
3.4.21.45;

Protein crystallography data

The structure of The Structure of Complement Complex, PDB code: 5o32 was solved by X.Xue, J.Wu, F.Forneris, P.Gros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.13 / 4.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 116.370, 122.790, 157.200, 69.76, 76.10, 70.13
R / Rfree (%) 22.9 / 25.4

Calcium Binding Sites:

The binding sites of Calcium atom in the The Structure of Complement Complex (pdb code 5o32). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the The Structure of Complement Complex, PDB code: 5o32:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 1 out of 6 in the The Structure of Complement Complex


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 Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca701

b:61.8
occ:1.00
 OD1 A:ASP557 2.3 69.1 1.0
OD1 A:ASP554 2.4 64.5 1.0
CG A:ASP557 3.2 70.4 1.0
CG A:ASP554 3.2 65.7 1.0
OD2 A:ASP554 3.3 67.1 1.0
O A:VAL555 3.4 67.7 1.0
OD2 A:ASP557 3.5 69.7 1.0
O A:PRO527 3.7 61.1 1.0
OE2 A:GLU621 3.7 60.7 1.0
CB A:PRO527 4.1 62.1 1.0
C A:PRO527 4.4 61.6 1.0
N A:VAL555 4.6 64.9 1.0
CB A:ASP557 4.6 73.8 1.0
C A:VAL555 4.6 68.8 1.0
CB A:ASP554 4.7 66.3 1.0
CA A:PRO527 4.7 63.1 1.0
CD A:GLU621 4.7 61.8 1.0
N A:ASP557 4.8 75.1 1.0

Calcium binding site 2 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 2 out of 6 in the The Structure of Complement Complex


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 Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca401

b:0.8
occ:1.00
 O D:TYR276 2.3 0.7 1.0
OD1 D:ASN279 2.3 0.6 1.0
OE1 D:GLU290 2.4 0.6 1.0
OD2 D:ASP283 2.4 0.5 1.0
O D:GLU281 2.4 0.8 1.0
OD2 D:ASP289 2.5 0.2 1.0
CD D:GLU290 2.8 0.2 1.0
CG D:GLU290 3.2 0.4 1.0
CG D:ASP283 3.3 0.1 1.0
CG D:ASN279 3.3 0.3 1.0
C D:TYR276 3.5 0.5 1.0
CG D:ASP289 3.6 0.9 1.0
C D:GLU281 3.6 0.0 1.0
OE2 D:GLU290 3.7 0.1 1.0
ND2 D:ASN279 3.7 0.1 1.0
OD1 D:ASP283 4.0 0.5 1.0
CB D:ASP283 4.0 0.1 1.0
N D:ASP283 4.1 0.3 1.0
N D:GLU281 4.3 0.2 1.0
OD1 D:ASP289 4.4 0.2 1.0
CB D:ASP289 4.4 0.0 1.0
N D:GLN277 4.4 0.8 1.0
CA D:TYR276 4.4 0.4 1.0
N D:ASN279 4.5 0.1 1.0
CA D:GLN277 4.5 0.8 1.0
CA D:GLU281 4.5 0.2 1.0
CB D:ASN279 4.5 0.8 1.0
N D:VAL282 4.6 0.6 1.0
N D:CYS278 4.6 0.1 1.0
CB D:TYR276 4.6 0.7 1.0
CB D:GLU290 4.7 0.2 1.0
CA D:VAL282 4.7 0.8 1.0
C D:VAL282 4.7 0.2 1.0
CA D:ASP283 4.7 1.0 1.0
C D:GLN277 4.8 0.8 1.0
CB D:GLU281 4.9 0.0 1.0
O D:ASP289 4.9 0.4 1.0
C D:ASP289 5.0 0.1 1.0
CA D:ASN279 5.0 0.1 1.0
N D:GLY280 5.0 1.0 1.0

Calcium binding site 3 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 3 out of 6 in the The Structure of Complement Complex


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 Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca402

b:0.4
occ:1.00
 O D:ILE244 2.1 1.0 1.0
O D:LYS239 2.3 0.4 1.0
OE2 D:GLU253 2.4 0.9 1.0
OD2 D:ASP252 2.4 0.8 1.0
OD1 D:ASP242 2.4 0.6 1.0
OD1 D:ASP246 2.5 0.4 1.0
C D:ILE244 3.2 0.0 1.0
CG D:ASP252 3.2 0.1 1.0
CG D:ASP242 3.4 0.8 1.0
C D:LYS239 3.5 0.2 1.0
CD D:GLU253 3.5 0.8 1.0
CG D:ASP246 3.6 0.5 1.0
CA D:ALA240 3.8 0.8 1.0
OD2 D:ASP242 3.8 0.2 1.0
N D:ILE244 3.8 0.7 1.0
OD1 D:ASP252 3.8 0.9 1.0
CA D:ILE244 3.9 0.1 1.0
N D:CYS241 3.9 0.8 1.0
N D:ASP246 4.0 0.2 1.0
CB D:ILE244 4.1 0.1 1.0
N D:ALA240 4.1 0.7 1.0
N D:ASP242 4.1 0.8 1.0
C D:ALA240 4.1 0.4 1.0
CB D:ASP246 4.2 0.7 1.0
CB D:ASP252 4.2 0.2 1.0
CG D:GLU253 4.3 0.0 1.0
O D:ASP252 4.3 0.8 1.0
N D:ASN245 4.3 0.9 1.0
OE1 D:GLU253 4.4 0.2 1.0
CB D:ASP242 4.6 0.3 1.0
CA D:ASN245 4.6 0.8 1.0
OD2 D:ASP246 4.7 0.1 1.0
CA D:LYS239 4.7 0.7 1.0
N D:GLY243 4.7 0.7 1.0
CA D:ASP246 4.7 0.3 1.0
CA D:ASP242 4.8 0.7 1.0
C D:ASP252 4.8 1.0 1.0
C D:ASN245 4.8 0.4 1.0
CG2 D:ILE244 4.9 0.3 1.0
CA D:CYS241 4.9 1.0 1.0
C D:GLY243 4.9 0.3 1.0
CB D:ALA240 5.0 0.0 1.0

Calcium binding site 4 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 4 out of 6 in the The Structure of Complement Complex


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 Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca701

b:51.8
occ:1.00
 OD1 E:ASP557 2.3 77.3 1.0
OD1 E:ASP554 2.5 72.0 1.0
OD2 E:ASP554 3.0 75.6 1.0
CG E:ASP554 3.1 73.1 1.0
CG E:ASP557 3.2 78.9 1.0
O E:VAL555 3.4 72.7 1.0
OD2 E:ASP557 3.4 80.7 1.0
O E:PRO527 3.9 67.2 1.0
OE2 E:GLU621 3.9 66.0 1.0
CB E:PRO527 4.2 68.2 1.0
CB E:ASP557 4.5 78.5 1.0
C E:VAL555 4.6 71.1 1.0
C E:PRO527 4.6 65.8 1.0
CB E:ASP554 4.6 71.5 1.0
N E:VAL555 4.6 70.3 1.0
N E:ASP557 4.7 75.6 1.0
CA E:PRO527 4.9 65.3 1.0
CD E:GLU621 4.9 66.8 1.0
CA E:ASP557 5.0 75.1 1.0

Calcium binding site 5 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 5 out of 6 in the The Structure of Complement Complex


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 Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca401

b:93.4
occ:1.00
 O H:GLU281 2.3 99.2 1.0
OD2 H:ASP283 2.3 95.0 1.0
OD1 H:ASN279 2.3 98.8 1.0
O H:TYR276 2.4 98.8 1.0
OE1 H:GLU290 2.4 97.4 1.0
OD2 H:ASP289 2.4 93.7 1.0
CD H:GLU290 2.9 97.2 1.0
CG H:ASP283 3.1 94.8 1.0
CG H:GLU290 3.2 97.2 1.0
CG H:ASN279 3.3 98.8 1.0
C H:GLU281 3.5 99.4 1.0
CG H:ASP289 3.5 94.8 1.0
C H:TYR276 3.6 99.6 1.0
ND2 H:ASN279 3.6 98.1 1.0
OE2 H:GLU290 3.7 97.2 1.0
OD1 H:ASP283 3.8 94.2 1.0
CB H:ASP283 3.8 95.8 1.0
N H:ASP283 3.9 95.7 1.0
N H:GLU281 4.3 0.1 1.0
CB H:ASP289 4.3 96.2 1.0
CA H:GLU281 4.4 99.7 1.0
OD1 H:ASP289 4.4 95.0 1.0
N H:VAL282 4.4 97.4 1.0
CA H:TYR276 4.5 99.1 1.0
C H:VAL282 4.5 97.5 1.0
CA H:ASP283 4.5 95.9 1.0
CA H:VAL282 4.5 97.7 1.0
N H:GLN277 4.5 97.0 1.0
N H:ASN279 4.5 0.7 1.0
CB H:ASN279 4.5 99.7 1.0
CA H:GLN277 4.6 97.5 1.0
N H:CYS278 4.7 1.0 1.0
CB H:GLU281 4.7 99.4 1.0
CB H:TYR276 4.7 99.1 1.0
CB H:GLU290 4.7 98.0 1.0
O H:ASP289 4.9 96.2 1.0
C H:GLN277 4.9 97.3 1.0
C H:ASP289 4.9 96.0 1.0

Calcium binding site 6 out of 6 in 5o32

Go back to Calcium Binding Sites List in 5o32
Calcium binding site 6 out of 6 in the The Structure of Complement Complex


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of The Structure of Complement Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Ca402

b:0.4
occ:1.00
 O H:LYS239 2.3 0.5 1.0
OD1 H:ASP246 2.3 96.8 1.0
OE2 H:GLU253 2.4 98.0 1.0
OD2 H:ASP252 2.4 91.4 1.0
O H:ILE244 2.4 88.5 1.0
OD1 H:ASP242 2.4 99.8 1.0
CG H:ASP252 3.2 91.2 1.0
CG H:ASP242 3.3 0.3 1.0
C H:LYS239 3.5 0.2 1.0
C H:ILE244 3.5 87.4 1.0
CG H:ASP246 3.5 95.9 1.0
CD H:GLU253 3.5 95.9 1.0
OD2 H:ASP242 3.7 0.1 1.0
CA H:ALA240 3.8 0.5 1.0
OD1 H:ASP252 3.8 88.3 1.0
N H:CYS241 3.9 98.5 1.0
N H:ILE244 4.0 88.9 1.0
N H:ASP242 4.0 0.1 1.0
N H:ALA240 4.1 0.7 1.0
CA H:ILE244 4.1 87.8 1.0
CB H:ASP246 4.1 94.7 1.0
N H:ASP246 4.1 89.8 1.0
C H:ALA240 4.1 0.9 1.0
CB H:ASP252 4.1 95.3 1.0
CB H:ILE244 4.2 88.5 1.0
O H:ASP252 4.3 96.0 1.0
CG H:GLU253 4.3 93.2 1.0
OE1 H:GLU253 4.4 96.1 1.0
OD2 H:ASP246 4.5 96.1 1.0
CB H:ASP242 4.6 0.7 1.0
N H:ASN245 4.6 88.5 1.0
CA H:LYS239 4.6 0.9 1.0
CA H:ASP242 4.7 0.5 1.0
N H:GLY243 4.8 0.7 1.0
CA H:ASP246 4.8 90.7 1.0
C H:ASP252 4.8 94.2 1.0
CA H:CYS241 4.8 98.4 1.0
CA H:ASN245 4.9 88.0 1.0
C H:CYS241 4.9 98.2 1.0
CG2 H:ILE244 5.0 87.6 1.0
C H:ASN245 5.0 88.5 1.0

Reference:

X.Xue, J.Wu, D.Ricklin, F.Forneris, P.Di Crescenzio, C.Q.Schmidt, J.Granneman, T.H.Sharp, J.D.Lambris, P.Gros. Regulator-Dependent Mechanisms of C3B Processing By Factor I Allow Differentiation of Immune Responses. Nat. Struct. Mol. Biol. V. 24 643 2017.
ISSN: ESSN 1545-9985
PubMed: 28671664
DOI: 10.1038/NSMB.3427
Page generated: Sat Dec 12 05:41:00 2020

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