Calcium in PDB 7edd: Crystal Structure of A Serine Protease From Streptococcus Pyogenes

Enzymatic activity of Crystal Structure of A Serine Protease From Streptococcus Pyogenes

All present enzymatic activity of Crystal Structure of A Serine Protease From Streptococcus Pyogenes:
3.4.21.110;

Protein crystallography data

The structure of Crystal Structure of A Serine Protease From Streptococcus Pyogenes, PDB code: 7edd was solved by C.Jobichen, J.Sivaraman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.37 / 2.90
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 191.969, 191.969, 252.788, 90, 90, 120
R / Rfree (%) 19.5 / 25.5

Other elements in 7edd:

The structure of Crystal Structure of A Serine Protease From Streptococcus Pyogenes also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
Magnesium (Mg) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes (pdb code 7edd). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes, PDB code: 7edd:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 7edd

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Calcium binding site 1 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1704

b:114.6
occ:1.00
 CG A:GLU1431 4.3 66.3 1.0
ND2 A:ASN208 4.4 62.9 1.0
CD A:GLU1431 4.4 83.1 1.0
OE2 A:GLU1431 4.6 88.6 1.0
OE2 A:GLU204 4.9 81.1 1.0
OE1 A:GLU1431 5.0 86.8 1.0

Calcium binding site 2 out of 10 in 7edd

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Calcium binding site 2 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1705

b:111.3
occ:1.00
 NZ A:LYS1050 2.3 72.8 1.0
CE A:MSE1107 2.5 86.7 1.0
OE2 A:GLU1109 2.7 53.5 1.0
CE A:LYS1050 3.6 55.3 1.0
CD A:GLU1109 3.9 55.1 1.0
OG A:SER1052 3.9 68.9 1.0
CE2 A:PHE1083 3.9 69.5 1.0
C3 A:GOL1713 4.0 72.7 1.0
CD A:LYS1050 4.2 46.4 1.0
CZ A:PHE1083 4.2 66.1 1.0
SE A:MSE1107 4.5 95.9 1.0
OE1 A:GLU1109 4.7 61.6 1.0
NH2 A:ARG1049 4.7 41.0 1.0
O1 A:GOL1713 4.7 64.4 1.0
O3 A:GOL1713 4.8 68.0 1.0
C1 A:GOL1713 4.9 70.8 1.0
CB A:SER1052 4.9 62.0 1.0
CG A:GLU1109 4.9 45.4 1.0

Calcium binding site 3 out of 10 in 7edd

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Calcium binding site 3 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1706

b:39.5
occ:1.00
 OD2 A:ASP1017 2.0 41.3 1.0
OD2 A:ASP1110 2.3 39.9 1.0
O A:GLN1019 2.4 37.6 1.0
OD2 A:ASP1042 2.4 43.6 1.0
O A:ARG1043 2.5 41.0 1.0
OD1 A:ASP1042 2.6 49.4 1.0
CG A:ASP1042 2.8 47.4 1.0
CG A:ASP1017 3.0 41.7 1.0
OD1 A:ASP1017 3.4 37.2 1.0
CG A:ASP1110 3.4 41.2 1.0
C A:GLN1019 3.6 36.4 1.0
C A:ARG1043 3.6 40.9 1.0
CB A:ASP1110 3.8 42.3 1.0
ND2 A:ASN1114 4.1 34.8 1.0
N A:ARG1043 4.2 39.5 1.0
CB A:ASP1017 4.3 38.2 1.0
N A:GLN1019 4.3 39.7 1.0
CB A:ASP1042 4.3 42.1 1.0
CA A:GLN1019 4.3 34.5 1.0
CB A:GLN1019 4.3 35.3 1.0
CA A:GLY1044 4.5 35.0 1.0
CB A:ALA1046 4.5 34.9 1.0
N A:GLY1044 4.5 37.5 1.0
CA A:ARG1043 4.5 41.2 1.0
OD1 A:ASP1110 4.5 41.3 1.0
C A:LYS1020 4.5 43.3 1.0
CB A:ASN1114 4.6 35.5 1.0
N A:LYS1020 4.6 36.5 1.0
N A:PRO1021 4.7 40.3 1.0
CA A:LYS1020 4.7 39.7 1.0
CG A:ASN1114 4.8 37.2 1.0
O A:LYS1020 4.8 42.8 1.0
C A:GLY1044 4.8 38.6 1.0
N A:ALA1046 4.9 28.3 1.0
O A:GLY1044 4.9 44.8 1.0
C A:ASP1042 5.0 43.2 1.0
CA A:ASP1042 5.0 40.9 1.0

Calcium binding site 4 out of 10 in 7edd

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Calcium binding site 4 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1707

b:41.3
occ:1.00
 ND2 A:ASN910 2.3 43.8 1.0
O A:ASN914 2.4 37.3 1.0
O A:SER908 2.4 30.5 1.0
OD1 A:ASN910 2.4 40.2 1.0
OD1 A:ASP912 2.4 41.6 1.0
OD1 A:ASP916 2.5 41.5 1.0
OG A:SER908 2.5 38.2 1.0
CG A:ASN910 2.6 37.1 1.0
OD2 A:ASP912 3.0 40.1 1.0
CG A:ASP912 3.1 38.2 1.0
CB A:SER908 3.4 37.8 1.0
C A:SER908 3.5 35.0 1.0
C A:ASN914 3.5 41.8 1.0
CG A:ASP916 3.7 39.4 1.0
CA A:SER908 4.0 33.2 1.0
N A:ASN914 4.0 42.3 1.0
CB A:ASN910 4.1 29.4 1.0
CA A:ASN914 4.1 41.5 1.0
CB A:ASN914 4.2 39.8 1.0
OD2 A:ASP916 4.4 40.1 1.0
N A:ASN910 4.4 32.7 1.0
C A:GLN915 4.5 36.9 1.0
CB A:ASP912 4.5 38.0 1.0
O A:GLN915 4.5 32.9 1.0
N A:ASP916 4.5 36.5 1.0
N A:ASP912 4.6 39.5 1.0
N A:SER908 4.6 31.6 1.0
N A:GLN915 4.7 37.1 1.0
CA A:ASP916 4.7 27.9 1.0
N A:PRO909 4.7 40.0 1.0
OD1 A:ASN1114 4.7 44.6 1.0
N A:ASN913 4.8 36.5 1.0
CB A:ASP916 4.8 25.3 1.0
CA A:ASN910 4.8 31.6 1.0
O A:ALA1112 4.9 40.1 1.0
O A:GLY1113 4.9 38.4 1.0
CA A:ASP912 4.9 38.0 1.0

Calcium binding site 5 out of 10 in 7edd

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Calcium binding site 5 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1708

b:99.2
occ:1.00
 OD1 A:ASN914 2.9 46.6 1.0
ND2 A:ASN914 3.6 42.5 1.0
CG A:ASN914 3.6 43.1 1.0
O1 A:GOL1713 4.1 64.4 1.0
CE1 A:HIS881 4.1 38.5 1.0
NE2 A:GLN915 4.4 43.3 1.0
CG A:GLN915 4.4 40.6 1.0
NE2 A:HIS881 4.5 38.6 1.0
CA A:GLY865 4.7 40.4 1.0
C1 A:GOL1713 4.7 70.8 1.0
CD A:GLN915 4.7 42.0 1.0

Calcium binding site 6 out of 10 in 7edd

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Calcium binding site 6 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1709

b:89.2
occ:1.00
 OE1 A:GLU1537 2.8 50.7 1.0
CG A:PRO1562 3.6 39.9 1.0
CD A:GLU1537 3.7 53.2 1.0
OE2 A:GLU1537 3.9 56.3 1.0
CD A:PRO1562 4.6 35.3 1.0
CB A:ALA1491 4.6 41.1 1.0
CB A:PRO1562 4.7 30.3 1.0

Calcium binding site 7 out of 10 in 7edd

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Calcium binding site 7 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1710

b:98.3
occ:1.00
 NE2 A:GLN819 2.3 68.7 1.0
OE2 A:GLU821 2.7 52.4 1.0
CD A:GLN819 3.6 56.3 1.0
O A:TYR1526 3.7 48.6 1.0
CD A:GLU821 3.8 47.1 1.0
OE1 A:GLU821 4.1 46.1 1.0
ND2 A:ASN705 4.2 48.1 1.0
CG A:GLN819 4.3 51.2 1.0
OE1 A:GLN819 4.5 52.1 1.0
CG2 A:VAL1527 4.6 32.9 1.0
CB A:GLN819 4.9 46.2 1.0
C A:TYR1526 4.9 43.3 1.0
CA A:VAL1527 5.0 40.5 1.0
ND2 A:ASN822 5.0 43.9 1.0

Calcium binding site 8 out of 10 in 7edd

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Calcium binding site 8 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1711

b:94.9
occ:1.00
 CE2 A:TYR610 2.5 53.9 1.0
CG2 A:THR604 2.5 56.4 1.0
OH A:TYR610 2.8 60.6 1.0
OG A:SER160 2.9 56.2 1.0
CZ A:TYR610 3.1 53.5 1.0
CB A:SER160 3.3 56.2 1.0
O A:PHE301 3.5 56.1 1.0
CD2 A:TYR610 3.7 47.3 1.0
CB A:THR604 4.1 44.0 1.0
CB A:PHE301 4.1 48.1 1.0
CB A:SER291 4.1 56.1 1.0
C A:PHE301 4.3 48.4 1.0
CA A:SER160 4.4 57.5 1.0
CE1 A:TYR610 4.4 53.7 1.0
CE1 A:HIS158 4.5 64.5 1.0
CA A:GLY289 4.7 49.1 1.0
CA A:PHE301 4.7 48.3 1.0
CA A:THR604 4.7 50.5 1.0
N A:THR604 4.8 46.8 1.0
N A:SER291 4.8 52.0 1.0
CG A:TYR610 4.9 47.6 1.0
ND1 A:HIS158 4.9 59.4 1.0
N A:PHE301 4.9 55.4 1.0
OG1 A:THR604 4.9 40.3 1.0
N A:ASN290 5.0 54.3 1.0

Calcium binding site 9 out of 10 in 7edd

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Calcium binding site 9 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1712

b:45.3
occ:1.00
 ND2 A:ASN1192 2.3 49.6 1.0
OD1 A:ASN1192 2.3 53.2 1.0
OD1 A:ASP1194 2.3 44.2 1.0
O A:ASN1196 2.3 39.6 1.0
O A:SER1190 2.5 37.2 1.0
CG A:ASN1192 2.6 50.1 1.0
OG A:SER1190 2.7 39.4 1.0
OD1 A:ASP1198 2.7 39.5 1.0
OD2 A:ASP1194 3.0 42.3 1.0
CG A:ASP1194 3.0 44.3 1.0
CB A:SER1190 3.5 40.5 1.0
C A:ASN1196 3.5 38.1 1.0
C A:SER1190 3.6 43.1 1.0
O A:GLY1381 3.8 45.9 1.0
CG A:ASP1198 4.0 42.6 1.0
CA A:SER1190 4.0 40.8 1.0
O A:LYS1197 4.0 42.8 1.0
CB A:ASN1192 4.1 36.5 1.0
C A:LYS1197 4.2 39.4 1.0
CA A:ASN1196 4.3 35.9 1.0
N A:ASN1196 4.3 39.6 1.0
CB A:ASN1196 4.4 35.4 1.0
CB A:ASP1194 4.4 40.5 1.0
N A:ASP1198 4.5 37.5 1.0
N A:ASN1192 4.5 43.6 1.0
N A:SER1190 4.5 37.8 1.0
N A:LYS1197 4.6 36.3 1.0
C A:GLY1381 4.6 38.2 1.0
CA A:ASP1198 4.6 33.6 1.0
O A:ALA1380 4.7 46.4 1.0
N A:ASP1194 4.8 48.0 1.0
N A:PRO1191 4.8 44.2 1.0
CA A:LYS1197 4.8 33.7 1.0
OD2 A:ASP1198 4.8 40.5 1.0
CA A:ASN1192 4.9 39.1 1.0
CB A:ASP1198 4.9 33.3 1.0
CB A:LYS1197 5.0 36.5 1.0

Calcium binding site 10 out of 10 in 7edd

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Calcium binding site 10 out of 10 in the Crystal Structure of A Serine Protease From Streptococcus Pyogenes


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Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of A Serine Protease From Streptococcus Pyogenes within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1722

b:91.1
occ:1.00
 ND1 A:HIS1498 2.3 70.7 1.0
CE1 A:HIS1498 2.4 67.4 1.0
CG A:HIS1498 2.5 63.3 1.0
NE2 A:HIS1498 2.6 77.8 1.0
CD2 A:HIS1498 2.8 81.3 1.0
CB A:HIS1498 3.4 54.5 1.0
O A:GLY1004 3.8 39.0 1.0
O1 A:GOL1715 3.9 38.5 1.0
CA A:GLY1004 4.2 33.8 1.0
C A:GLY1004 4.3 39.0 1.0
CA A:HIS1498 4.5 49.5 1.0
CB A:ALA1530 4.7 36.8 1.0
CG1 A:VAL1527 4.8 36.1 1.0
CG2 A:THR1496 4.9 34.3 1.0

Reference:

C.Jobichen, T.Ying Chong, T.Hui Ling, J.Sivaraman. The Autocatalytic Cleavage Domain Is Not Required For the Activity of Scpc, A Virulence Protease From Streptococcus Pyogenes : A Structural Insight. Biochemistry 2021.
ISSN: ISSN 0006-2960
PubMed: 33929828
DOI: 10.1021/ACS.BIOCHEM.1C00185
Page generated: Sat Jul 10 11:29:16 2021

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